├── .codecov.yml ├── .github └── workflows │ ├── deploy.yml │ └── run_tests.yml ├── .gitignore ├── .pylintrc ├── .readthedocs.yaml ├── .zenodo.json ├── LICENSE ├── README.md ├── bin └── martinize2 ├── doc ├── Makefile └── source │ ├── _static │ └── .empty_for_git │ ├── _templates │ └── layout.html │ ├── conf.py │ ├── data.rst │ ├── file_formats.rst │ ├── general_overview.rst │ ├── graph_algorithms.rst │ ├── gromacs_variables.rst │ ├── index.rst │ ├── martinize2_workflow.rst │ ├── processors.rst │ ├── technical_background.rst │ └── tutorials │ ├── 6_adding_residues_links │ ├── files │ │ ├── ala-sep-ala.pdb │ │ ├── force_fields │ │ │ ├── charmm │ │ │ │ ├── sep.ff │ │ │ │ └── sep.rtp │ │ │ └── martini3001 │ │ │ │ └── sep.ff │ │ └── mappings │ │ │ └── sep.charmm36.map │ └── index.rst │ ├── 7_adding_modifications │ ├── files │ │ ├── ala-sep-ala.pdb │ │ ├── force_fields │ │ │ ├── charmm │ │ │ │ └── mods.ff │ │ │ └── martini3001 │ │ │ │ └── modification.ff │ │ └── mappings │ │ │ └── SEP.mapping │ └── index.rst │ ├── basic_usage.rst │ ├── elastic_examples.png │ ├── elastic_networks.rst │ ├── go_models.rst │ ├── index.rst │ ├── mutations_and_modifications.rst │ └── water_biasing.rst ├── maintainers ├── head_template_data ├── head_template_py ├── releasing.md └── vim │ └── syntax │ ├── README.md │ └── ff.vim ├── pyproject.toml ├── requirements-docs.txt ├── requirements-tests.txt ├── setup.cfg ├── setup.py └── vermouth ├── __init__.py ├── citation_parser.py ├── data ├── __init__.py ├── citations.bib ├── data.py ├── force_fields │ ├── amber │ │ ├── aminoacids.rtp │ │ └── modifications.ff │ ├── charmm │ │ ├── aminoacids.rtp │ │ ├── lipidations.rtp │ │ ├── modifications.ff │ │ └── small_molecule_charmm.ff │ ├── elnedyn21 │ │ ├── aminoacids.ff │ │ ├── citations.bib │ │ ├── general.ff │ │ └── modifications.ff │ ├── elnedyn22 │ │ ├── aminoacids.ff │ │ ├── citations.bib │ │ ├── general.ff │ │ └── modifications.ff │ ├── elnedyn22p │ │ ├── aminoacids.ff │ │ ├── citations.bib │ │ ├── general.ff │ │ └── modifications.ff │ ├── gromos │ │ ├── aminoacids.rtp │ │ ├── cofactors.ff │ │ └── modifications.ff │ ├── martini22 │ │ ├── aminoacids.ff │ │ ├── citations.bib │ │ ├── general.ff │ │ ├── modifications.ff │ │ └── nucleotides.ff │ ├── martini22p │ │ ├── aminoacids.ff │ │ ├── citations.bib │ │ ├── general.ff │ │ └── modifications.ff │ ├── martini3001 │ │ ├── aminoacids.ff │ │ ├── citations.bib │ │ ├── general.ff │ │ ├── modifications.ff │ │ └── small_molecule_martini3.ff │ ├── martini30b32 │ │ ├── aminoacids.ff │ │ ├── citations.bib │ │ ├── modifications.ff │ │ └── small_molecules.ff │ ├── martini30dev │ │ ├── aminoacids.ff │ │ ├── citations.bib │ │ └── modifications.ff │ └── martini3IDP │ │ ├── aminoacids.ff │ │ ├── citations.bib │ │ ├── general.ff │ │ └── modifications.ff ├── mappings │ ├── ala.charmm36.map │ ├── ala.gromos.map │ ├── arg.charmm36.map │ ├── arg.charmm36.martini22p.map │ ├── arg.gromos.map │ ├── asn.charmm36.map │ ├── asn.charmm36.martini22p.map │ ├── asn.gromos.map │ ├── asp.charmm36.map │ ├── asp.charmm36.martini22p.map │ ├── asp.gromos.map │ ├── asp0.gromos.map │ ├── chol.charmm36.map │ ├── cys.charmm36.map │ ├── cys.gromos.map │ ├── dmpc.charmm36.map │ ├── dopc.charmm36.map │ ├── dppc.charmm36.map │ ├── dppg.charmm36.map │ ├── elnedyn │ │ ├── ala.charmm36.map │ │ ├── arg.charmm36.map │ │ ├── asn.charmm36.map │ │ ├── asp.charmm36.map │ │ ├── chol.charmm36.map │ │ ├── cys.charmm36.map │ │ ├── dmpc.charmm36.map │ │ ├── dopc.charmm36.map │ │ ├── dppc.charmm36.map │ │ ├── dppg.charmm36.map │ │ ├── elnedyn22p │ │ │ ├── arg.charmm36.elnedyn22p.map │ │ │ ├── asn.charmm36.elnedyn22p.map │ │ │ ├── asp.charmm36.elnedyn22p.map │ │ │ ├── gln.charmm36.elnedyn22p.map │ │ │ ├── glu.charmm36.elnedyn22p.map │ │ │ ├── lys.charmm36.elnedyn22p.map │ │ │ ├── ser.charmm36.elnedyn22p.map │ │ │ └── thr.charmm36.elnedyn22p.map │ │ ├── gln.charmm36.map │ │ ├── glu.charmm36.map │ │ ├── gly.charmm36.map │ │ ├── his.charmm36.map │ │ ├── ile.charmm36.map │ │ ├── leu.charmm36.map │ │ ├── lys.charmm36.map │ │ ├── met.charmm36.map │ │ ├── modifications.elnedyn21.mapping │ │ ├── modifications.elnedyn22.mapping │ │ ├── modifications.elnedyn22p.mapping │ │ ├── phe.charmm36.map │ │ ├── popc.charmm36.map │ │ ├── pope.charmm36.map │ │ ├── popg.charmm36.map │ │ ├── pops.charmm36.map │ │ ├── pro.charmm36.map │ │ ├── ser.charmm36.map │ │ ├── thr.charmm36.map │ │ ├── trp.charmm36.map │ │ ├── tyr.charmm36.map │ │ └── val.charmm36.map │ ├── elnedyn21 │ │ ├── ala.charmm36.map │ │ ├── arg.charmm36.elnedyn22p.map │ │ ├── arg.charmm36.map │ │ ├── asn.charmm36.elnedyn22p.map │ │ ├── asn.charmm36.map │ │ ├── asp.charmm36.elnedyn22p.map │ │ ├── asp.charmm36.map │ │ ├── cys.charmm36.map │ │ ├── gln.charmm36.elnedyn22p.map │ │ ├── gln.charmm36.map │ │ ├── glu.charmm36.elnedyn22p.map │ │ ├── glu.charmm36.map │ │ ├── gly.charmm36.map │ │ ├── his.charmm36.map │ │ ├── ile.charmm36.map │ │ ├── leu.charmm36.map │ │ ├── lys.charmm36.elnedyn22p.map │ │ ├── lys.charmm36.map │ │ ├── met.charmm36.map │ │ ├── modifications.mapping │ │ ├── phe.charmm36.map │ │ ├── pro.charmm36.map │ │ ├── ser.charmm36.elnedyn22p.map │ │ ├── ser.charmm36.map │ │ ├── thr.charmm36.elnedyn22p.map │ │ ├── thr.charmm36.map │ │ ├── trp.charmm36.map │ │ ├── tyr.charmm36.map │ │ └── val.charmm36.map │ ├── fmn.gromos.map │ ├── gln.charmm36.map │ ├── gln.charmm36.martini22p.map │ ├── gln.gromos.map │ ├── glu.charmm36.map │ ├── glu.charmm36.martini22p.map │ ├── glu.gromos.map │ ├── glu0.gromos.map │ ├── gly.charmm36.map │ ├── gly.gromos.map │ ├── his.charmm.mapping │ ├── his.charmm36.map │ ├── his.gromos.map │ ├── his.gromos.mapping │ ├── hsd.charmm36.map │ ├── hse.charmm36.map │ ├── hsp.charmm36.map │ ├── ile.charmm36.map │ ├── ile.gromos.map │ ├── leu.charmm36.map │ ├── leu.gromos.map │ ├── lys.charmm36.map │ ├── lys.charmm36.martini22p.map │ ├── lys.gromos.map │ ├── martini3001 │ │ ├── ala.amber.map │ │ ├── ala.charmm36.map │ │ ├── antr.charmm36.map │ │ ├── arg.amber.map │ │ ├── arg.charmm36.map │ │ ├── ash.amber.map │ │ ├── asn.amber.map │ │ ├── asn.charmm36.map │ │ ├── asp.amber.map │ │ ├── asp.charmm36.map │ │ ├── aspp.charmm36.map │ │ ├── bald.charmm36.map │ │ ├── benz.charmm36.map │ │ ├── c3.charmm36.map │ │ ├── chxe.charmm36.map │ │ ├── cpen.charmm36.map │ │ ├── cume.charmm36.map │ │ ├── cys.amber.map │ │ ├── cys.charmm36.map │ │ ├── cysf.map │ │ ├── cysg.map │ │ ├── cysp.map │ │ ├── diol.charmm36.map │ │ ├── diox.charmm36.map │ │ ├── dman.charmm36.map │ │ ├── eben.charmm36.map │ │ ├── fura.charmm36.map │ │ ├── glh.amber.map │ │ ├── gln.amber.map │ │ ├── gln.charmm36.map │ │ ├── glu.amber.map │ │ ├── glu.charmm36.map │ │ ├── glup.charmm36.map │ │ ├── gly.amber.map │ │ ├── gly.charmm36.map │ │ ├── glym.map │ │ ├── hid.amber.map │ │ ├── hie.amber.map │ │ ├── hip.amber.map │ │ ├── his.amber.map │ │ ├── his.charmm36.map │ │ ├── hsd.charmm36.map │ │ ├── hse.charmm36.map │ │ ├── hsp.charmm36.map │ │ ├── ile.amber.map │ │ ├── ile.charmm36.map │ │ ├── imia.charmm36.map │ │ ├── inda.charmm36.map │ │ ├── indo.charmm36.map │ │ ├── leu.amber.map │ │ ├── leu.charmm36.map │ │ ├── lsn.charmm36.map │ │ ├── lyn.amber.map │ │ ├── lys.amber.map │ │ ├── lys.charmm36.map │ │ ├── mboa.charmm36.map │ │ ├── mcpe.charmm36.map │ │ ├── meob.charmm36.map │ │ ├── met.amber.map │ │ ├── met.charmm36.map │ │ ├── mind.charmm36.map │ │ ├── modifications.amber.mapping │ │ ├── modifications.charmm36.mapping │ │ ├── mxyl.charmm36.map │ │ ├── naft.charmm36.map │ │ ├── nitb.charmm36.map │ │ ├── oxyl.charmm36.map │ │ ├── pcro.charmm36.map │ │ ├── phe.amber.map │ │ ├── phe.charmm36.map │ │ ├── phen.charmm36.map │ │ ├── phmk.charmm36.map │ │ ├── prld.charmm36.map │ │ ├── pro.amber.map │ │ ├── pro.charmm36.map │ │ ├── pxyl.charmm36.map │ │ ├── pyr1.charmm36.map │ │ ├── pyrd.charmm36.map │ │ ├── pyrl.charmm36.map │ │ ├── pyrm.charmm36.map │ │ ├── qinl.charmm36.map │ │ ├── ser.amber.map │ │ ├── ser.charmm36.map │ │ ├── sm139.charmm36.map │ │ ├── styr.charmm36.map │ │ ├── thaz.charmm36.map │ │ ├── thf.charmm36.map │ │ ├── thip.charmm36.map │ │ ├── thp.charmm36.map │ │ ├── thr.amber.map │ │ ├── thr.charmm36.map │ │ ├── tolu.charmm36.map │ │ ├── trp.amber.map │ │ ├── trp.charmm36.map │ │ ├── tyr.amber.map │ │ ├── tyr.charmm36.map │ │ ├── val.amber.map │ │ ├── val.charmm36.map │ │ ├── zimi.charmm36.map │ │ ├── zthp.charmm36.map │ │ └── zthz.charmm36.map │ ├── martini30b32 │ │ ├── ala.charmm36.map │ │ ├── arg.charmm36.map │ │ ├── asn.charmm36.map │ │ ├── asp.charmm36.map │ │ ├── benz.charmm36.map │ │ ├── cys.charmm36.map │ │ ├── gln.charmm36.map │ │ ├── glu.charmm36.map │ │ ├── gly.charmm36.map │ │ ├── his.charmm36.map │ │ ├── hsd.charmm36.map │ │ ├── ile.charmm36.map │ │ ├── leu.charmm36.map │ │ ├── lys.charmm36.map │ │ ├── met.charmm36.map │ │ ├── modifications.mapping │ │ ├── phe.charmm36.map │ │ ├── pro.charmm36.map │ │ ├── ser.charmm36.map │ │ ├── thr.charmm36.map │ │ ├── trp.charmm36.map │ │ ├── tyr.charmm36.map │ │ └── val.charmm36.map │ ├── martini3IDP │ │ ├── ala.amber.map │ │ ├── ala.charmm36.map │ │ ├── arg.amber.map │ │ ├── arg.charmm36.map │ │ ├── asn.amber.map │ │ ├── asn.charmm36.map │ │ ├── asp.amber.map │ │ ├── asp.charmm36.map │ │ ├── aspp.charmm36.map │ │ ├── cys.amber.map │ │ ├── cys.charmm36.map │ │ ├── gln.amber.map │ │ ├── gln.charmm36.map │ │ ├── glu.amber.map │ │ ├── glu.charmm36.map │ │ ├── glup.charmm36.map │ │ ├── gly.amber.map │ │ ├── gly.charmm36.map │ │ ├── hid.amber.map │ │ ├── hie.amber.map │ │ ├── hip.amber.map │ │ ├── his.amber.map │ │ ├── his.charmm36.map │ │ ├── hsd.charmm36.map │ │ ├── hse.charmm36.map │ │ ├── hsp.charmm36.map │ │ ├── ile.amber.map │ │ ├── ile.charmm36.map │ │ ├── leu.amber.map │ │ ├── leu.charmm36.map │ │ ├── lsn.charmm36.map │ │ ├── lyn.amber.map │ │ ├── lys.amber.map │ │ ├── lys.charmm36.map │ │ ├── met.amber.map │ │ ├── met.charmm36.map │ │ ├── modifications.amber.mapping │ │ ├── modifications.charmm36.mapping │ │ ├── phe.amber.map │ │ ├── phe.charmm36.map │ │ ├── pro.amber.map │ │ ├── pro.charmm36.map │ │ ├── ser.amber.map │ │ ├── ser.charmm36.map │ │ ├── sp2.charmm36.map │ │ ├── thr.amber.map │ │ ├── thr.charmm36.map │ │ ├── trp.amber.map │ │ ├── trp.charmm36.map │ │ ├── tyr.amber.map │ │ ├── tyr.charmm36.map │ │ ├── val.amber.map │ │ └── val.charmm36.map │ ├── met.charmm36.map │ ├── met.gromos.map │ ├── modifications.gromos.mapping │ ├── modifications.mapping │ ├── nad.gromos.map │ ├── phe.charmm36.map │ ├── phe.gromos.map │ ├── popc.charmm36.map │ ├── pope.charmm36.map │ ├── popg.charmm36.map │ ├── pops.charmm36.map │ ├── pro.charmm36.map │ ├── pro.gromos.map │ ├── ser.charmm36.map │ ├── ser.charmm36.martini22p.map │ ├── ser.gromos.map │ ├── thr.charmm36.map │ ├── thr.charmm36.martini22p.map │ ├── thr.gromos.map │ ├── tpp.gromos.map │ ├── trp.charmm36.map │ ├── trp.gromos.map │ ├── tyr.charmm36.map │ ├── tyr.gromos.map │ ├── val.charmm36.map │ └── val.gromos.map └── quotes.txt ├── dssp ├── __init__.py └── dssp.py ├── edge_tuning.py ├── ffinput.py ├── file_writer.py ├── forcefield.py ├── geometry.py ├── gmx ├── __init__.py ├── gro.py ├── itp.py ├── itp_read.py ├── rtp.py └── topology.py ├── graph_utils.py ├── graphing └── grappa.py ├── ismags.py ├── log_helpers.py ├── map_input.py ├── map_parser.py ├── molecule.py ├── parser_utils.py ├── pdb ├── __init__.py ├── cif.py └── pdb.py ├── processors ├── __init__.py ├── add_molecule_edges.py ├── annotate_idrs.py ├── annotate_mut_mod.py ├── apply_posres.py ├── apply_rubber_band.py ├── attach_mass.py ├── average_beads.py ├── canonicalize_modifications.py ├── cif_reader.py ├── do_links.py ├── do_mapping.py ├── gro_reader.py ├── locate_charge_dummies.py ├── make_bonds.py ├── merge_all_molecules.py ├── merge_chains.py ├── name_moltype.py ├── pdb_reader.py ├── processor.py ├── quote.py ├── rename_modified_residues.py ├── repair_graph.py ├── set_molecule_meta.py ├── sort_molecule_atoms.py ├── stash_attributes.py ├── tune_cystein_bridges.py └── water_bias.py ├── rcsu ├── __init__.py ├── contact_map.py ├── go_pipeline.py ├── go_structure_bias.py ├── go_utils.py └── go_vs_includes.py ├── selectors.py ├── system.py ├── tests ├── __init__.py ├── data │ ├── 1UBQ.cif │ ├── 1UBQ.pdb │ ├── 1UBQ_nocell_occupancy.cif │ ├── 1bta.pdb │ ├── 1bta_mutated.pdb │ ├── 2QWO.pdb │ ├── 2dn2.pdb │ ├── 6E8W.pdb │ ├── ala5.pdb │ ├── ala5_cg.pdb │ ├── cif_missing_atomname.cif │ ├── cif_missing_resname.cif │ ├── dna-short.pdb │ ├── dssp_tests │ │ ├── dssp_1bta.ssd │ │ ├── mini-protein1_betasheet.pdb.v2.2.1-3b2-deb_cv1.ssd │ │ ├── mini-protein1_betasheet.pdb.v3.0.0-3b1-deb_cv1.ssd │ │ ├── mini-protein2_helix.pdb.v2.2.1-3b2-deb_cv1.ssd │ │ ├── mini-protein2_helix.pdb.v3.0.0-3b1-deb_cv1.ssd │ │ ├── mini-protein3_trp-cage.pdb.v2.2.1-3b2-deb_cv1.ssd │ │ └── mini-protein3_trp-cage.pdb.v3.0.0-3b1-deb_cv1.ssd │ ├── force_fields │ │ ├── martini-test │ │ │ └── aminoacids.ff │ │ ├── pepplane │ │ │ ├── ala.ff │ │ │ ├── general.ff │ │ │ └── modifications.ff │ │ └── universal-test │ │ │ ├── aminoacids.rtp │ │ │ └── modifications.ff │ ├── heme.pdb │ ├── integration_tests │ │ ├── tier-0 │ │ │ ├── dipro-termini │ │ │ │ ├── README │ │ │ │ ├── aa.pdb │ │ │ │ └── martinize2 │ │ │ │ │ ├── cg.pdb │ │ │ │ │ ├── citation │ │ │ │ │ ├── command │ │ │ │ │ ├── molecule_0.itp │ │ │ │ │ └── topol.top │ │ │ ├── mini-protein1_betasheet │ │ │ │ ├── README │ │ │ │ ├── aa.pdb │ │ │ │ └── martinize2 │ │ │ │ │ ├── cg.pdb │ │ │ │ │ ├── chain_A.ssd │ │ │ │ │ ├── citation │ │ │ │ │ ├── command │ │ │ │ │ ├── molecule_0.itp │ │ │ │ │ ├── screen.output │ │ │ │ │ └── topol.top │ │ │ ├── mini-protein2_helix │ │ │ │ ├── README │ │ │ │ ├── aa.pdb │ │ │ │ └── martinize2 │ │ │ │ │ ├── cg.pdb │ │ │ │ │ ├── chain_A.ssd │ │ │ │ │ ├── citation │ │ │ │ │ ├── command │ │ │ │ │ ├── molecule_0.itp │ │ │ │ │ ├── screen.output │ │ │ │ │ └── topol.top │ │ │ └── mini-protein3_trp-cage │ │ │ │ ├── README │ │ │ │ ├── aa.pdb │ │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── chain_A.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ ├── screen.output │ │ │ │ └── topol.top │ │ └── tier-1 │ │ │ ├── 1UBQ │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ └── topol.top │ │ │ ├── 1mj5-charmm │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── cg.top │ │ │ │ ├── chain_.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ └── screen.output │ │ │ ├── 1mj5 │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── cg.top │ │ │ │ ├── chain_.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ └── screen.output │ │ │ ├── 3i40 │ │ │ ├── 3i40.pdb │ │ │ ├── README │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── cg.top │ │ │ │ ├── chain_A.ssd │ │ │ │ ├── chain_C.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── insulin_dimer.itp │ │ │ │ ├── molecule_0.itp │ │ │ │ └── screen.output │ │ │ ├── 6LFO_gap │ │ │ ├── 6LFO_gap.pdb │ │ │ ├── README │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── cg.top │ │ │ │ ├── chain_R.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ └── screen.output │ │ │ ├── EN_chain │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── cg.top │ │ │ │ ├── chain_A.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ └── screen.output │ │ │ ├── EN_region │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── cg.top │ │ │ │ ├── chain_A.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ └── screen.output │ │ │ ├── bpti │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── chain_A.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ ├── screen.output │ │ │ │ └── topol.top │ │ │ ├── hst5 │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ ├── topol.top │ │ │ │ ├── virtual_sites_atomtypes.itp │ │ │ │ └── virtual_sites_nonbond_params.itp │ │ │ ├── lysozyme │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── chain_A.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ ├── screen.output │ │ │ │ ├── test.itp │ │ │ │ └── topol.top │ │ │ ├── lysozyme_ENbias │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ ├── map.map │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ ├── topol.top │ │ │ │ ├── virtual_sites_atomtypes.itp │ │ │ │ └── virtual_sites_nonbond_params.itp │ │ │ ├── lysozyme_GO │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ ├── map.map │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── go_atomtypes.itp │ │ │ │ ├── go_nbparams.itp │ │ │ │ ├── molecule_0.itp │ │ │ │ └── topol.top │ │ │ ├── lysozyme_GO_internal │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── go_atomtypes.itp │ │ │ │ ├── go_nbparams.itp │ │ │ │ ├── martinize_contact_map.out │ │ │ │ ├── molecule.itp │ │ │ │ └── topol.top │ │ │ ├── lysozyme_GObias │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ ├── map.map │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── go_atomtypes.itp │ │ │ │ ├── go_nbparams.itp │ │ │ │ ├── molecule_0.itp │ │ │ │ └── topol.top │ │ │ ├── lysozyme_prot │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ ├── cg.pdb │ │ │ ├── chain_A.ssd │ │ │ ├── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── chain_A.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ ├── screen.output │ │ │ │ ├── test.itp │ │ │ │ └── topol.top │ │ │ ├── molecule_0.itp │ │ │ └── topol.top │ │ │ ├── prot_modf_charmm │ │ │ ├── README │ │ │ ├── input.pdb │ │ │ └── martinize2 │ │ │ │ ├── cg.pdb │ │ │ │ ├── cg.top │ │ │ │ ├── chain_.ssd │ │ │ │ ├── citation │ │ │ │ ├── command │ │ │ │ ├── molecule_0.itp │ │ │ │ ├── screen.output │ │ │ │ └── sys.top │ │ │ └── villin │ │ │ ├── README │ │ │ ├── aa.pdb │ │ │ └── martinize2 │ │ │ ├── cg.pdb │ │ │ ├── citation │ │ │ ├── command │ │ │ ├── molecule_0.itp │ │ │ ├── screen.output │ │ │ └── topol.top │ ├── mappings │ │ └── universal-test │ │ │ ├── martini-test │ │ │ └── ser.mapping │ │ │ └── pepplane │ │ │ ├── ala.mapping │ │ │ └── modifications.mapping │ ├── multiple.cif │ ├── test_molecule_contacts.out │ └── tri_alanine.pdb ├── datafiles.py ├── gmx │ ├── test_gro.py │ ├── test_itp.py │ └── test_topology.py ├── helper_functions.py ├── integration_tests │ ├── __init__.py │ └── test_integration.py ├── molecule_strategies.py ├── pdb │ ├── test_cif.py │ ├── test_read_pdb.py │ └── test_write_pdb.py ├── rcsu │ ├── test_contact_map.py │ ├── test_go_structure_bias.py │ ├── test_go_utils.py │ └── test_read_go_map.py ├── test_add_molecule_edges.py ├── test_annotate_idrs.py ├── test_annotate_mut_mod.py ├── test_apply_posres.py ├── test_apply_rubber_band.py ├── test_average_beads.py ├── test_cif_reader.py ├── test_do_mapping.py ├── test_dssp.py ├── test_edge_tuning.py ├── test_ff_files.py ├── test_ffinput.py ├── test_file_writer.py ├── test_forcefield.py ├── test_geometry.py ├── test_graph_utils.py ├── test_grappa.py ├── test_ismags.py ├── test_itp_files.py ├── test_links.py ├── test_logging.py ├── test_make_bonds.py ├── test_map_input.py ├── test_map_parser.py ├── test_mapping_integrative.py ├── test_merge_chains.py ├── test_molecule.py ├── test_name_moltype.py ├── test_native_forcefield.py ├── test_ptm_detection.py ├── test_repair_graph.py ├── test_section_parser.py ├── test_selectors.py ├── test_set_molecule_meta.py ├── test_sort_molecule_atoms.py ├── test_stash_attributes.py ├── test_system.py ├── test_tune_cystein_bridges.py ├── test_utils.py ├── test_version.py ├── test_vs_generation.py └── test_water_bias.py ├── truncating_formatter.py └── utils.py /.codecov.yml: -------------------------------------------------------------------------------- 1 | coverage: 2 | range: 50..100 3 | round: nearest 4 | precision: 1 5 | status: 6 | project: 7 | default: 8 | target: 80 9 | threshold: 1 10 | patch: 11 | default: 12 | target: 90 13 | 14 | ignore: 15 | - vermouth/tests 16 | comment: off 17 | 18 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | test.pdb 2 | **/__pycache__ 3 | **.pyc 4 | **.bak 5 | \#* 6 | 7 | **.lprof 8 | 9 | .eggs/** 10 | *.swp 11 | .pytest_cache 12 | *.egg-info 13 | .coverage 14 | .hypothesis 15 | 16 | htmlcov 17 | 18 | doc/build 19 | doc/source/api 20 | doc/source/.doctrees 21 | 22 | .idea/ 23 | -------------------------------------------------------------------------------- /.readthedocs.yaml: -------------------------------------------------------------------------------- 1 | # .readthedocs.yaml 2 | # Read the Docs configuration file 3 | # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details 4 | 5 | # Required 6 | version: 2 7 | 8 | # Set the version of Python and other tools you might need 9 | build: 10 | os: ubuntu-22.04 11 | tools: 12 | python: "3" 13 | 14 | formats: 15 | - pdf 16 | 17 | # Build documentation in the docs/ directory with Sphinx 18 | sphinx: 19 | builder: html 20 | fail_on_warning: true 21 | configuration: doc/source/conf.py 22 | 23 | # We recommend specifying your dependencies to enable reproducible builds: 24 | # https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html 25 | python: 26 | install: 27 | - method: pip 28 | path: . 29 | - requirements: requirements-docs.txt -------------------------------------------------------------------------------- /.zenodo.json: -------------------------------------------------------------------------------- 1 | { 2 | "creators": [ 3 | { 4 | "orcid": "0000-0001-9273-4850", 5 | "name": "Peter C. Kroon" 6 | }, 7 | { 8 | "orcid": "0000-0001-6979-1363", 9 | "name": "Fabian Gr\"unewald" 10 | }, 11 | { 12 | "orcid": "0000-0003-0343-7796", 13 | "name": "Jonathan Barnoud" 14 | }, 15 | { 16 | "orcid": "0000-0003-0660-1301", 17 | "name": "Paulo C. T. Souza" 18 | }, 19 | { 20 | "orcid": "0000-0002-6345-0266", 21 | "name": "Tsjerk A. Wassenaar" 22 | }, 23 | { 24 | "orcid": " 0000-0001-8423-5277", 25 | "name": "Siewert J. Marrink" 26 | } 27 | 28 | ] 29 | } 30 | -------------------------------------------------------------------------------- /doc/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | SPHINXPROJ = VerMoUTH 8 | SOURCEDIR = source 9 | BUILDDIR = build 10 | 11 | # Put it first so that "make" without argument is like "make help". 12 | help: 13 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 14 | 15 | .PHONY: help Makefile 16 | 17 | # Catch-all target: route all unknown targets to Sphinx using the new 18 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 19 | %: Makefile 20 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) -------------------------------------------------------------------------------- /doc/source/_static/.empty_for_git: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/80c692afbc0976e487f3835c0f9da279003a25fe/doc/source/_static/.empty_for_git -------------------------------------------------------------------------------- /doc/source/_templates/layout.html: -------------------------------------------------------------------------------- 1 | {% extends '!layout.html' %} 2 | 3 | {% block footer %} 4 | 5 |
{{ project }} {{ version }}
6 | {{ super() }} 7 | {% endblock %} 8 | -------------------------------------------------------------------------------- /doc/source/index.rst: -------------------------------------------------------------------------------- 1 | .. VerMoUTH documentation master file, created by 2 | sphinx-quickstart on Fri Jun 22 14:51:23 2018. 3 | You can adapt this file completely to your liking, but it should at least 4 | contain the root `toctree` directive. 5 | 6 | Welcome to VerMoUTH's documentation! 7 | ==================================== 8 | 9 | .. toctree:: 10 | :maxdepth: 2 11 | :caption: Contents: 12 | 13 | general_overview 14 | martinize2_workflow 15 | technical_background 16 | file_formats 17 | tutorials/index 18 | api/modules 19 | gromacs_variables 20 | 21 | 22 | Indices and tables 23 | ================== 24 | 25 | * :ref:`genindex` 26 | * :ref:`modindex` 27 | * :ref:`search` 28 | 29 | -------------------------------------------------------------------------------- /doc/source/processors.rst: -------------------------------------------------------------------------------- 1 | Processor 2 | ========= 3 | :class:`Processors ` are relatively 4 | simple. They form the fundamental steps of the martinize2 pipeline. Processors 5 | are called via their :meth:`~vermouth.processors.processor.Processor.run_system` 6 | method. The default implementation of this method iterates over the molecules 7 | in the system, and runs the :meth:`~vermouth.processors.processor.Processor.run_molecule` 8 | method on them. This means that implementations of Processors must implement 9 | either a ``run_system`` method, or a ``run_molecule`` method. If the processor 10 | can be run on independent molecules the ``run_molecule`` method is preferred; 11 | ``run_system`` should be used only for cases where the problem at hand cannot 12 | be separated in tasks-per-molecule. 13 | 14 | In their ``run_molecule`` method Processor implementations are free to either 15 | modify :class:`molecules ` or create new ones. 16 | Either way, they must return a :class:`~vermouth.molecule.Molecule`. The 17 | ``run_system`` will be called with a :class:`~vermouth.system.System`, which 18 | will be modified in place. 19 | -------------------------------------------------------------------------------- /doc/source/technical_background.rst: -------------------------------------------------------------------------------- 1 | Technical background 2 | ==================== 3 | Here we will provide some additional technical background about the chosen data 4 | structures and graph algorithms. 5 | 6 | .. toctree:: 7 | processors 8 | data 9 | graph_algorithms -------------------------------------------------------------------------------- /doc/source/tutorials/6_adding_residues_links/files/force_fields/charmm/sep.ff: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | SEP 3 3 | 4 | [ atoms ] 5 | 1 N 1 SEP N 1 0 6 | 2 H 1 SEP HN 2 0 7 | 3 C 1 SEP CA 3 0 8 | 4 H 1 SEP HA 4 0 9 | 5 C 1 SEP CB 5 0 10 | 6 H 1 SEP HB1 6 0 11 | 7 H 1 SEP HB2 7 0 12 | 8 O 1 SEP OG 8 0 13 | 9 C 1 SEP C 9 0 14 | 10 O 1 SEP O 10 0 15 | 11 P 1 SEP P 11 0 16 | 12 O 1 SEP O1 12 0 17 | 13 O 1 SEP O2 13 0 18 | 14 O 1 SEP O3 14 -1 19 | 20 | [ bonds ] 21 | 3 5 22 | 5 8 23 | 1 2 24 | 1 3 25 | 3 9 26 | 3 4 27 | 5 6 28 | 5 7 29 | 9 10 30 | 8 11 31 | 11 12 32 | 11 13 33 | 11 14 34 | -------------------------------------------------------------------------------- /doc/source/tutorials/6_adding_residues_links/files/force_fields/martini3001/sep.ff: -------------------------------------------------------------------------------- 1 | ;[ macros ] 2 | ;protein_resnames "GLY|ALA|CYS|VAL|LEU|ILE|MET|PRO|HYP|ASN|GLN|ASP|ASPP|ASH|GLU|GLUP|GLH|THR|SER|LYS|LSN|LYN|ARG|HSE|HIS|HSD|HSP|HID|HIP|HIE|PHE|TYR|TRP|SEP" 3 | ;protein_resnames_non_pro "GLY|ALA|CYS|VAL|LEU|ILE|MET|ASN|GLN|ASP|ASPP|ASH|GLU|GLUP|GLH|THR|SER|LYS|LSN|LYN|ARG|HSE|HIS|HSD|HSP|HID|HIP|HIE|PHE|TYR|TRP|SEP" 4 | ;prot_default_bb_type P2 5 | ;stiff_fc 1000000 6 | 7 | ;;; PHOSPHOSERINE 8 | [ moleculetype ] 9 | SEP 1 10 | 11 | [ warning ] 12 | THESE PARAMETERS ARE FOR DEMONSTRATION PURPOSES ONLY. DO NOT USE. 13 | 14 | [ atoms ] 15 | ; id type resnr residue atom cgnr charge 16 | 1 P2 1 SEP BB 1 0 17 | 2 Q5n 1 SEP SC1 1 -1 18 | 19 | [ bonds ] 20 | BB SC1 1 0.33 5000 21 | 22 | [ link ] 23 | [ warning ] 24 | THESE PARAMETERS ARE FOR DEMONSTRATION PURPOSES ONLY. DO NOT USE. 25 | [ atoms ] 26 | -BB {"resname": "ALA"} 27 | BB {"resname": "SEP"} 28 | SC1 {"resname": "SEP"} 29 | +BB {"resname": "ALA"} 30 | [ bonds ] 31 | BB +BB 1 0.35 4000 32 | BB -BB 1 0.35 4000 33 | [ angles ] 34 | -BB BB +BB 10 100 20 35 | -BB BB SC1 2 100 25 36 | -------------------------------------------------------------------------------- /doc/source/tutorials/6_adding_residues_links/files/mappings/sep.charmm36.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | SEP 3 | 4 | [ from ] 5 | charmm 6 | 7 | [ to ] 8 | martini3001 9 | 10 | [ martini ] 11 | BB SC1 12 | 13 | [ mapping ] 14 | charmm 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 HN BB 19 | 3 CA BB 20 | 4 HA !BB 21 | 5 CB BB SC1 22 | 6 HB1 !SC1 23 | 7 HB2 !SC1 24 | 8 OG SC1 25 | 9 C BB 26 | 10 O BB 27 | 11 P SC1 28 | 12 O1 SC1 29 | 13 O2 SC1 30 | 14 O3 SC1 31 | -------------------------------------------------------------------------------- /doc/source/tutorials/7_adding_modifications/files/force_fields/charmm/mods.ff: -------------------------------------------------------------------------------- 1 | [ modification ] 2 | SER-phos 3 | [ atoms ] 4 | O1 {"element": "O", "PTM_atom": true} 5 | O2 {"element": "O", "PTM_atom": true} 6 | O3 {"element": "O", "PTM_atom": true} 7 | P {"element": "P", "PTM_atom": true} 8 | OG {"element": "O"} 9 | HG1 {"element": "H", "replace": {"atomname": null}} 10 | [ edges ] 11 | OG P 12 | OG HG1 13 | P O1 14 | P O2 15 | P O3 16 | -------------------------------------------------------------------------------- /doc/source/tutorials/7_adding_modifications/files/force_fields/martini3001/modification.ff: -------------------------------------------------------------------------------- 1 | [ modification ] 2 | SER-PO4 3 | [ atoms ] 4 | BB {"PTM_atom": false} 5 | SC1 {"PTM_atom": false, "resname": "SER", "replace": {"atype": "Q5n", "charge": -1}} 6 | [ edges ] 7 | BB SC1 8 | [ bonds ] 9 | BB SC1 1 0.33 5000 10 | 11 | -------------------------------------------------------------------------------- /doc/source/tutorials/7_adding_modifications/files/mappings/SEP.mapping: -------------------------------------------------------------------------------- 1 | [ modification ] 2 | [ from ] 3 | charmm 4 | [ to ] 5 | martini3001 6 | [ from blocks ] 7 | SER-phos 8 | [ to blocks ] 9 | SER-PO4 10 | [ from nodes ] 11 | N 12 | HN 13 | CA 14 | HA 15 | C 16 | O 17 | CB 18 | HB1 19 | HB2 20 | [ from edges ] 21 | N HN 22 | N CA 23 | CA HA 24 | CA C 25 | C O 26 | CA CB 27 | CB HB1 28 | CB HB2 29 | CB OG 30 | [ mapping ] 31 | N BB 32 | HN BB 33 | CA BB 34 | HA BB 0 35 | C BB 36 | O BB 37 | CB BB 38 | CB SC1 39 | HB1 SC1 0 40 | HB2 SC1 0 41 | OG SC1 42 | P SC1 43 | O1 SC1 44 | O2 SC1 45 | O3 SC1 46 | -------------------------------------------------------------------------------- /doc/source/tutorials/elastic_examples.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/marrink-lab/vermouth-martinize/80c692afbc0976e487f3835c0f9da279003a25fe/doc/source/tutorials/elastic_examples.png -------------------------------------------------------------------------------- /doc/source/tutorials/index.rst: -------------------------------------------------------------------------------- 1 | Tutorials 2 | ========= 3 | This page contains several examples of how martinize2 can be used to convert 4 | proteins from atomistic to a martini3 representation. 5 | 6 | You can find further examples on how to use martinize2 in the martinize-examples 7 | repository: https://github.com/marrink-lab/martinize-examples 8 | 9 | .. Organize the tutorials in directories, so it's easier to keep their files 10 | together 11 | 12 | .. toctree:: 13 | basic_usage 14 | elastic_networks 15 | go_models 16 | water_biasing 17 | mutations_and_modifications 18 | 6_adding_residues_links/index 19 | 7_adding_modifications/index 20 | -------------------------------------------------------------------------------- /maintainers/head_template_data: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | -------------------------------------------------------------------------------- /maintainers/head_template_py: -------------------------------------------------------------------------------- 1 | # Copyright 2018 University of Groningen 2 | # 3 | # Licensed under the Apache License, Version 2.0 (the "License"); 4 | # you may not use this file except in compliance with the License. 5 | # You may obtain a copy of the License at 6 | # 7 | # http://www.apache.org/licenses/LICENSE-2.0 8 | # 9 | # Unless required by applicable law or agreed to in writing, software 10 | # distributed under the License is distributed on an "AS IS" BASIS, 11 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | # See the License for the specific language governing permissions and 13 | # limitations under the License. 14 | 15 | -------------------------------------------------------------------------------- /maintainers/releasing.md: -------------------------------------------------------------------------------- 1 | # Making a release 2 | 3 | Releases are deployed by Travis to peterkroon's PyPI, but only for tagged 4 | commits. This requires "build on push" is enabled on Travis, otherwise those 5 | don't get built at all. However, since we dev on branches in the main repo we 6 | only want Travis to build for master, and anything that looks like a SemVer 7 | version tag ('v1.2.3\[-prerelease\]\[+metadata\]'). Hence the ugly regex in the 8 | Travis yaml. (Note: PBR doesn't seem to be able to deal with all prerelease and 9 | metadata options allowed by SemVer) 10 | 11 | To make a release: 12 | - Implement your awesome feature, including docs. 13 | - Make a PR of your feature, get it reviewed and make sure Travis passes. 14 | - Get your feature merged in master 15 | - Create a tag: `git tag v0.5.0 -a`. Come up with a sane version number. 16 | - Push the tag: `git push --tags`. 17 | - Profit. 18 | 19 | Note that Travis will build releases *twice*. Once because something is pushed 20 | to master, and once because it's a tagged commit. But since we don't release 21 | too often this is OK. Also, if this is to change Travis should first come up 22 | with way better documentation. 23 | 24 | -------------------------------------------------------------------------------- /maintainers/vim/syntax/README.md: -------------------------------------------------------------------------------- 1 | VIM syntax highlighting for vermouth file formats 2 | ================================================= 3 | 4 | This directory contains syntax highlighting rules for VIM to handle vermouth 5 | files. Install them by copying the content of this directory in 6 | `~/.vim/syntax/`. To activate the highlighting, you should copy the following 7 | lines in `~/.vimrc`: 8 | 9 | ``` 10 | " Highlighting for vermouth force field files 11 | au BufNewFile,BufRead *.ff set syntax=ff 12 | ``` 13 | -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- 1 | [build-system] 2 | requires = [ 3 | "wheel", 4 | "setuptools >= 30.3.0", 5 | "pbr", 6 | ] 7 | build-backend = "pbr.build" 8 | 9 | [tool.pytest.ini_options] 10 | addopts = "--import-mode=importlib" 11 | testpaths = ["vermouth/tests"] 12 | python_files = "test_*.py" 13 | 14 | [tool.coverage.run] 15 | branch = true 16 | omit = ["vermouth/tests/*", "vermouth/redistributed/*", '*/bin/pytest'] 17 | source_pkgs = ["vermouth"] 18 | -------------------------------------------------------------------------------- /requirements-docs.txt: -------------------------------------------------------------------------------- 1 | sphinx >= 8.2.1 2 | pbr 3 | setuptools >= 30.3.0 4 | 5 | numpy 6 | networkx 7 | scipy 8 | -------------------------------------------------------------------------------- /requirements-tests.txt: -------------------------------------------------------------------------------- 1 | attrs >= 19.2.0 # Comes from hypothesis, but is not automatically picked up by 2 | # pip. See pypa/pip#7135 and pypa/pip#988 3 | pytest 4 | coverage 5 | pytest-cov 6 | pylint 7 | hypothesis 8 | hypothesis-networkx 9 | codecov 10 | mdtraj 11 | pycifrw 12 | -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- 1 | # Copyright 2018 University of Groningen 2 | # 3 | # Licensed under the Apache License, Version 2.0 (the "License"); 4 | # you may not use this file except in compliance with the License. 5 | # You may obtain a copy of the License at 6 | # 7 | # http://www.apache.org/licenses/LICENSE-2.0 8 | # 9 | # Unless required by applicable law or agreed to in writing, software 10 | # distributed under the License is distributed on an "AS IS" BASIS, 11 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | # See the License for the specific language governing permissions and 13 | # limitations under the License.import os 14 | 15 | import os 16 | from setuptools import setup 17 | 18 | def package_files(directory): 19 | paths = [] 20 | for (path, directories, filenames) in os.walk(directory): 21 | for filename in filenames: 22 | paths.append(os.path.join('..', path, filename)) 23 | return paths 24 | 25 | setup( 26 | package_data={'': package_files('vermouth/data') 27 | + package_files('vermouth/tests/data'),}, 28 | scripts=['bin/martinize2', ], 29 | pbr=True, 30 | ) 31 | -------------------------------------------------------------------------------- /vermouth/data/__init__.py: -------------------------------------------------------------------------------- 1 | # Copyright 2025 University of Groningen 2 | # 3 | # Licensed under the Apache License, Version 2.0 (the "License"); 4 | # you may not use this file except in compliance with the License. 5 | # You may obtain a copy of the License at 6 | # 7 | # http://www.apache.org/licenses/LICENSE-2.0 8 | # 9 | # Unless required by applicable law or agreed to in writing, software 10 | # distributed under the License is distributed on an "AS IS" BASIS, 11 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | # See the License for the specific language governing permissions and 13 | # limitations under the License. 14 | 15 | from .data import * 16 | -------------------------------------------------------------------------------- /vermouth/data/citations.bib: -------------------------------------------------------------------------------- 1 | @article{MDTraj, 2 | title={MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories}, 3 | author={McGibbon, Robert T. and Beauchamp, Kyle A. and Harrigan, Matthew P. and Klein, Christoph and Swails, Jason M. and Hernández, Carlos X. and Schwantes, Christian R. and Wang, Lee-Ping and Lane, Thomas J. and Pande, Vijay S.}, 4 | journal={Biophysical Journal}, 5 | volume={109}, 6 | number={8}, 7 | pages={1528 -- 1532}, 8 | year={2015}, 9 | doi={10.1016/j.bpj.2015.08.015} 10 | } 11 | @article{vermouth, 12 | title={Martinize2 and Vermouth: Unified Framework for Topology Generation}, 13 | url={http://dx.doi.org/10.7554/eLife.90627.2}, 14 | doi={10.7554/elife.90627.2}, 15 | journal={elife}, 16 | volume={12}, 17 | pages={RP90627} 18 | publisher={eLife Sciences Publications, Ltd}, 19 | author={Kroon, Peter C and Grunewald, F and Barnoud, J and van Tilburg, M and Souza, Paulo CT and Wassenaar, Tsjerk A and Marrink, Siewert J}, 20 | year={2024}, 21 | month=jun 22 | } 23 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn21/general.ff: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ variables ] 16 | center_weight "mass" 17 | bb_atomname "BB" 18 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn21/modifications.ff: -------------------------------------------------------------------------------- 1 | [ modification ] 2 | C-ter 3 | [ atoms ] 4 | BB {"replace": {"atype": "Qa", "charge": -1}} 5 | 6 | [ modification ] 7 | N-ter 8 | [ atoms ] 9 | BB {"replace": {"atype": "Qd", "charge": 1}} 10 | 11 | [ modification ] 12 | zwitter 13 | [ atoms ] 14 | BB {"replace": {"atype": "Qda"}} 15 | 16 | [ modification ] 17 | COOH-ter 18 | [ atoms ] 19 | BB {"replace": {"atype": "P5", "charge": 0}} 20 | 21 | [ modification ] 22 | NH2-ter 23 | [ atoms ] 24 | BB {"replace": {"atype": "P5", "charge": 0}} 25 | 26 | [ modification ] 27 | LYS-LSN 28 | [ atoms ] 29 | SC2 {"resname": "LYS", "replace": {"atype": "P1", "charge": 0}} 30 | 31 | [ modification ] 32 | LYS-HZ3 33 | [ atoms ] 34 | SC2 {"replace": {"resname": "LYS"}} 35 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn22/general.ff: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ variables ] 16 | center_weight "mass" 17 | bb_atomname "BB" 18 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn22/modifications.ff: -------------------------------------------------------------------------------- 1 | [ modification ] 2 | C-ter 3 | [ atoms ] 4 | BB {"replace": {"atype": "Qa", "charge": -1}} 5 | 6 | [ modification ] 7 | N-ter 8 | [ atoms ] 9 | BB {"replace": {"atype": "Qd", "charge": 1}} 10 | 11 | [ modification ] 12 | zwitter 13 | [ atoms ] 14 | BB {"replace": {"atype": "Qda"}} 15 | 16 | [ modification ] 17 | COOH-ter 18 | [ atoms ] 19 | BB {"replace": {"atype": "P5", "charge": 0}} 20 | 21 | [ modification ] 22 | NH2-ter 23 | [ atoms ] 24 | BB {"replace": {"atype": "P5", "charge": 0}} 25 | 26 | [ modification ] 27 | ASP-HD1 28 | [ atoms ] 29 | SC1 {"resname": "ASP", "replace": {"atype": "P3", "charge": 0}} 30 | 31 | [ modification ] 32 | ASP-HD2 33 | [ atoms ] 34 | SC1 {"resname": "ASP", "replace": {"atype": "P3", "charge": 0}} 35 | 36 | [ modification ] 37 | LYS-LSN 38 | [ atoms ] 39 | SC2 {"resname": "LYS", "replace": {"atype": "P1", "charge": 0}} 40 | 41 | [ modification ] 42 | LYS-HZ3 43 | [ atoms ] 44 | SC2 {"replace": {"resname": "LYS"}} 45 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn22p/general.ff: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ variables ] 16 | center_weight "mass" 17 | bb_atomname "BB" -------------------------------------------------------------------------------- /vermouth/data/force_fields/elnedyn22p/modifications.ff: -------------------------------------------------------------------------------- 1 | [ modification ] 2 | C-ter 3 | [ atoms ] 4 | BB {"replace": {"atype": "Qa", "charge": -1}} 5 | 6 | [ modification ] 7 | N-ter 8 | [ atoms ] 9 | BB {"replace": {"atype": "Qd", "charge": 1}} 10 | 11 | [ modification ] 12 | zwitter 13 | [ atoms ] 14 | BB {"replace": {"atype": "Qda"}} 15 | 16 | [ modification ] 17 | COOH-ter 18 | [ atoms ] 19 | BB {"replace": {"atype": "P5", "charge": 0}} 20 | 21 | [ modification ] 22 | NH2-ter 23 | [ atoms ] 24 | BB {"replace": {"atype": "P5", "charge": 0}} 25 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/gromos/modifications.ff: -------------------------------------------------------------------------------- 1 | [ modification ] 2 | C-ter 3 | [ atoms ] 4 | CA {"element": "C"} 5 | C {"element": "C"} 6 | O {"element": "O"} 7 | OXT {"element": "O", "PTM_atom": true} 8 | [ edges ] 9 | CA C 10 | C O 11 | C OXT 12 | 13 | [ modification ] 14 | N-ter 15 | [ atoms ] 16 | CA {"element": "C"} 17 | N {"element": "N"} 18 | HN2 {"element": "H", "PTM_atom": true, "replace": {"atomname": "HN2"}} 19 | HN3 {"element": "H", "PTM_atom": true, "replace": {"atomname": "HN3"}} 20 | [ edges ] 21 | N CA 22 | N HN2 23 | N HN3 24 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini22/general.ff: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ variables ] 16 | center_weight "mass" 17 | bb_atomname "BB" 18 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini22/modifications.ff: -------------------------------------------------------------------------------- 1 | [ modification ] 2 | C-ter 3 | [ atoms ] 4 | BB {"replace": {"atype": "Qa", "charge": -1}} 5 | 6 | [ modification ] 7 | N-ter 8 | [ atoms ] 9 | BB {"replace": {"atype": "Qd", "charge": 1}} 10 | 11 | [ modification ] 12 | zwitter 13 | [ atoms ] 14 | BB {"replace": {"atype": "Qda"}} 15 | 16 | [ modification ] 17 | COOH-ter 18 | [ atoms ] 19 | BB {"replace": {"atype": "P5", "charge": 0}} 20 | 21 | [ modification ] 22 | NH2-ter 23 | [ atoms ] 24 | BB {"replace": {"atype": "P5", "charge": 0}} 25 | 26 | [ modification ] 27 | TYRPHOS 28 | [ atoms ] 29 | SC3 {"replace": {"atype": "SNda"}} 30 | PO4 {"atype": "Qa", "charge": "-1", "PTM_atom": true} 31 | [ bonds ] 32 | SC3 PO4 1 0.47 1250 {"comment": "phospho"} 33 | [ edges ] 34 | SC3 PO4 35 | 36 | [ modification ] 37 | LYS-LSN 38 | [ atoms ] 39 | SC2 {"resname": "LYS", "replace": {"atype": "P1", "charge": 0}} 40 | 41 | [ modification ] 42 | LYS-HZ3 43 | [ atoms ] 44 | SC2 {"replace": {"resname": "LYS"}} 45 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini22p/general.ff: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ variables ] 16 | center_weight "mass" 17 | bb_atomname "BB" 18 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini22p/modifications.ff: -------------------------------------------------------------------------------- 1 | [ modification ] 2 | C-ter 3 | [ atoms ] 4 | BB {"replace": {"atype": "Qa", "charge": -1}} 5 | 6 | [ modification ] 7 | N-ter 8 | [ atoms ] 9 | BB {"replace": {"atype": "Qd", "charge": 1}} 10 | 11 | [ modification ] 12 | zwitter 13 | [ atoms ] 14 | BB {"replace": {"atype": "Qda"}} 15 | 16 | [ modification ] 17 | COOH-ter 18 | [ atoms ] 19 | BB {"replace": {"atype": "P5", "charge": 0}} 20 | 21 | [ modification ] 22 | NH2-ter 23 | [ atoms ] 24 | BB {"replace": {"atype": "P5", "charge": 0}} 25 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini3001/general.ff: -------------------------------------------------------------------------------- 1 | ; Copyright 2020 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ variables ] 16 | center_weight "mass" 17 | regular "0.47" 18 | small "0.41" 19 | tiny "0.34" 20 | water_type "W" 21 | bb_atomname "BB" 22 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini30b32/citations.bib: -------------------------------------------------------------------------------- 1 | @misc{Martini3Beta, 2 | title={Martini 3-Open Beta-Release}, 3 | author={Souza, Paulo C T and Marrink, Siewert Jan}, 4 | year={2020} 5 | } 6 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini30b32/modifications.ff: -------------------------------------------------------------------------------- 1 | [ modification ] 2 | C-ter 3 | [ atoms ] 4 | BB {"replace": {"atype": "Qn", "charge": -1}} 5 | 6 | [ modification ] 7 | N-ter 8 | [ atoms ] 9 | BB {"replace": {"atype": "Qp", "charge": 1}} 10 | 11 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini30b32/small_molecules.ff: -------------------------------------------------------------------------------- 1 | [ moleculetype ] 2 | BENZ 1 3 | [ atoms ] 4 | 1 TC4 1 BENZ R1 1 0.0 5 | 2 TC4 1 BENZ R2 2 0.0 6 | 3 TC4 1 BENZ R3 3 0.0 7 | [ constraints ] 8 | 0 1 1 0.290 {} 9 | 1 2 1 0.290 {} 10 | 0 2 1 0.290 {} 11 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini30dev/citations.bib: -------------------------------------------------------------------------------- 1 | @misc{Martini3Beta, 2 | title={Martini 3-Open Beta-Release}, 3 | author={Souza, Paulo C T and Marrink, Siewert Jan}, 4 | year={2020} 5 | } 6 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini30dev/modifications.ff: -------------------------------------------------------------------------------- 1 | [ modification ] 2 | C-ter 3 | [ atoms ] 4 | BB {"replace": {"atype": "Q1", "charge": -1}} 5 | 6 | [ modification ] 7 | N-ter 8 | [ atoms ] 9 | BB {"replace": {"atype": "Q1", "charge": 1}} 10 | 11 | [ modification ] 12 | COOH-ter 13 | [ atoms ] 14 | BB {"replace": {"atype": "P5", "charge": 0}} 15 | 16 | [ modification ] 17 | NH2-ter 18 | [ atoms ] 19 | BB {"replace": {"atype": "P4", "charge": 0}} 20 | -------------------------------------------------------------------------------- /vermouth/data/force_fields/martini3IDP/general.ff: -------------------------------------------------------------------------------- 1 | ; Copyright 2020 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ variables ] 16 | center_weight "mass" 17 | regular "0.47" 18 | small "0.41" 19 | tiny "0.34" 20 | water_type "W" 21 | bb_atomname "BB" 22 | -------------------------------------------------------------------------------- /vermouth/data/mappings/ala.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ALA 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini22 23 | martini22p 24 | 25 | [ martini ] 26 | BB 27 | 28 | [ mapping ] 29 | charmm27 charmm36 30 | 31 | [ atoms ] 32 | 1 N BB 33 | 2 HN BB 34 | 3 CA BB 35 | 5 CB BB 36 | 9 C BB 37 | 10 O BB 38 | 39 | [ chiral ] 40 | CB CA N C 41 | HB1 CA N C 42 | HB2 CA N C 43 | HB3 CA N C 44 | 45 | [ chiral ] 46 | HA CA N CB C ; L-Ala 47 | ; HA CA N C CB ; D-Ala 48 | -------------------------------------------------------------------------------- /vermouth/data/mappings/ala.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | ALA 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB BB 21 | 5 C BB 22 | 6 O BB 23 | 24 | -------------------------------------------------------------------------------- /vermouth/data/mappings/arg.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | ARG 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 SC2 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB SC1 BB BB 21 | 5 CG SC1 SC1 BB 22 | 6 CD SC1 23 | 7 NE SC2 SC1 24 | 8 HE SC2 SC1 25 | 9 CZ SC2 26 | 10 NH1 SC2 27 | 11 HH11 SC2 28 | 12 HH12 SC2 29 | 13 NH2 SC2 30 | 14 HH21 SC2 31 | 15 HH22 SC2 32 | 16 C BB 33 | 17 O BB 34 | -------------------------------------------------------------------------------- /vermouth/data/mappings/asn.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | ASN 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB SC1 BB BB 21 | 5 CG SC1 SC1 BB 22 | 6 OD1 SC1 23 | 7 ND2 SC1 24 | 8 HD21 SC1 25 | 9 HD22 SC1 26 | 10 C BB 27 | 11 O BB 28 | 29 | -------------------------------------------------------------------------------- /vermouth/data/mappings/asp.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ASP 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini22 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | ; 4 HA BB 35 | 5 CB SC1 36 | ; 6 HB1 SC1 37 | ; 7 HB2 SC1 38 | 8 CG SC1 39 | 9 OD1 SC1 40 | 10 OD2 SC1 41 | ; 11 HD2 SC1 42 | 12 C BB 43 | 13 O BB 44 | 45 | [ chiral ] 46 | CB CA N C 47 | HB1 CA N C 48 | HB2 CA N C 49 | 50 | [ chiral ] 51 | HA CA N CB C ; L-Asp 52 | ; HA CA N C CB ; D-Asp 53 | -------------------------------------------------------------------------------- /vermouth/data/mappings/asp.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | ASP 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB SC1 BB BB 21 | 5 CG SC1 SC1 BB 22 | 6 OD1 SC1 23 | 7 OD2 SC1 24 | 8 C BB 25 | 9 O BB 26 | -------------------------------------------------------------------------------- /vermouth/data/mappings/asp0.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | ASP0 3 | 4 | [ martini ] 5 | BB SC1 6 | 7 | [ mapping ] 8 | gromos 9 | 10 | [ atoms ] 11 | 1 N BB 12 | 2 H BB 13 | 3 CA BB 14 | 4 CB SC1 BB BB 15 | 5 CG SC1 SC1 BB 16 | 6 OD1 SC1 17 | 7 OD2 SC1 18 | 7 HD2 SC1 19 | 8 C BB 20 | 9 O BB 21 | -------------------------------------------------------------------------------- /vermouth/data/mappings/cys.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | CYS 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini22 23 | martini22p 24 | 25 | [ martini ] 26 | BB SC1 27 | 28 | [ mapping ] 29 | charmm27 charmm36 30 | 31 | [ atoms ] 32 | 1 N BB 33 | 2 HN BB 34 | 3 CA BB 35 | 4 CB SC1 36 | 7 SG SC1 37 | 9 C BB 38 | 10 O BB 39 | 40 | [ chiral ] 41 | CB CA N C 42 | HB1 CA N C 43 | HB2 CA N C 44 | 45 | [ chiral ] 46 | HA CA N CB C ; L-Cys 47 | ; HA CA N C CB ; D-Cys 48 | -------------------------------------------------------------------------------- /vermouth/data/mappings/cys.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | CYS 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB SC1 BB 21 | 5 SG SC1 22 | 6 HG SC1 23 | 7 C BB 24 | 8 O BB 25 | 26 | -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/ala.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ALA 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | elnedyn21 23 | elnedyn22 24 | elnedyn22p 25 | 26 | [ martini ] 27 | BB 28 | 29 | [ mapping ] 30 | charmm27 charmm36 31 | 32 | [ atoms ] 33 | 1 N !BB 34 | 2 HN !BB 35 | 3 CA BB 36 | 5 CB !BB 37 | 9 C !BB 38 | 10 O !BB 39 | 40 | [ chiral ] 41 | CB CA N C 42 | HB1 CA N C 43 | HB2 CA N C 44 | HB3 CA N C 45 | 46 | [ chiral ] 47 | HA CA N CB C ; L-Ala 48 | ; HA CA N C CB ; D-Ala 49 | -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/cys.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | CYS 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | elnedyn21 23 | elnedyn22 24 | elnedyn22p 25 | 26 | [ martini ] 27 | BB SC1 28 | 29 | [ mapping ] 30 | charmm27 charmm36 31 | 32 | [ atoms ] 33 | 1 N !BB 34 | 2 HN !BB 35 | 3 CA BB 36 | 4 CB SC1 37 | 7 SG SC1 38 | 9 C !BB 39 | 10 O !BB 40 | 41 | [ chiral ] 42 | CB CA N C 43 | HB1 CA N C 44 | HB2 CA N C 45 | 46 | [ chiral ] 47 | HA CA N CB C ; L-Cys 48 | ; HA CA N C CB ; D-Cys 49 | -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/elnedyn22p/ser.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | SER 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | elnedyn22p 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N !BB 32 | 2 HN !BB 33 | 3 CA BB 34 | 5 CB SC1 35 | 8 OG SC1 36 | 9 HG1 SC1 37 | 10 C !BB 38 | 11 O !BB 39 | 40 | [ chiral ] 41 | CB CA N C 42 | HB1 CA N C 43 | HB2 CA N C 44 | 45 | [ chiral ] 46 | HA CA N CB C ; L-Ser 47 | ; HA CA N C CB ; D-Ser 48 | 49 | [ extra ] 50 | SCP SCN 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/gln.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | GLN 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | elnedyn21 23 | elnedyn22 24 | 25 | [ martini ] 26 | BB SC1 27 | 28 | [ mapping ] 29 | charmm27 charmm36 30 | 31 | [ atoms ] 32 | 1 N !BB 33 | 2 HN !BB 34 | 3 CA BB 35 | 4 CB SC1 36 | 5 CG SC1 37 | 6 CD SC1 38 | 7 OE1 SC1 39 | 8 NE2 SC1 40 | 9 HE21 SC1 41 | 10 HE22 SC1 42 | 11 C !BB 43 | 12 O !BB 44 | 45 | [ chiral ] 46 | CB CA N C 47 | HB1 CA N C 48 | HB2 CA N C 49 | 50 | [ chiral ] 51 | HA CA N CB C ; L-Gln 52 | ; HA CA N C CB ; D-Gln 53 | -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/gly.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | GLY 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | elnedyn21 23 | elnedyn22 24 | elnedyn22p 25 | 26 | [ martini ] 27 | BB 28 | 29 | [ mapping ] 30 | charmm27 charmm36 31 | 32 | [ atoms ] 33 | 1 N !BB 34 | 2 HN !BB 35 | 3 CA BB 36 | 9 C !BB 37 | 10 O !BB 38 | -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/pro.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | PRO 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | elnedyn21 23 | elnedyn22 24 | elnedyn22p 25 | 26 | [ martini ] 27 | BB SC1 28 | 29 | [ mapping ] 30 | charmm27 charmm36 31 | 32 | [ atoms ] 33 | 1 N !BB 34 | 2 CD SC1 35 | 3 CA BB 36 | 4 CB SC1 37 | 5 CG SC1 38 | 6 C !BB 39 | 7 O !BB 40 | 41 | [ chiral ] 42 | CB CA N C 43 | HB1 CA N C 44 | HB2 CA N C 45 | 46 | [ chiral ] 47 | HA CA N CB C ; L-Pro 48 | ; HA CA N C CB ; D-Pro 49 | -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/ser.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | SER 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | elnedyn21 23 | elnedyn22 24 | 25 | [ martini ] 26 | BB SC1 27 | 28 | [ mapping ] 29 | charmm27 charmm36 30 | 31 | [ atoms ] 32 | 1 N !BB 33 | 2 HN !BB 34 | 3 CA BB 35 | 5 CB SC1 36 | 8 OG SC1 37 | 9 HG1 SC1 38 | 10 C !BB 39 | 11 O !BB 40 | 41 | [ chiral ] 42 | CB CA N C 43 | HB1 CA N C 44 | HB2 CA N C 45 | 46 | [ chiral ] 47 | HA CA N CB C ; L-Ser 48 | ; HA CA N C CB ; D-Ser 49 | -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn/val.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | VAL 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | elnedyn21 23 | elnedyn22 24 | elnedyn22p 25 | 26 | [ martini ] 27 | BB SC1 28 | 29 | [ mapping ] 30 | charmm27 charmm36 31 | 32 | [ atoms ] 33 | 1 N !BB 34 | 2 HN !BB 35 | 3 CA BB 36 | 5 CB SC1 37 | 8 CG1 SC1 38 | 12 CG2 SC1 39 | 16 C !BB 40 | 17 O !BB 41 | -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/ala.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ALA 17 | 18 | [from] 19 | universal 20 | 21 | [to] 22 | elnedyn21 23 | elnedyn22 24 | elnedyn22p 25 | 26 | [ martini ] 27 | BB 28 | 29 | [ mapping ] 30 | charmm27 charmm36 31 | 32 | [ atoms ] 33 | 1 N !BB 34 | 2 HN !BB 35 | 3 CA BB 36 | 5 CB !BB 37 | 9 C !BB 38 | 10 O !BB 39 | 40 | [ chiral ] 41 | CB CA N C 42 | HB1 CA N C 43 | HB2 CA N C 44 | HB3 CA N C 45 | 46 | [ chiral ] 47 | HA CA N CB C ; L-Ala 48 | ; HA CA N C CB ; D-Ala 49 | -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/cys.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | CYS 17 | 18 | [from] 19 | universal 20 | 21 | [to] 22 | elnedyn21 23 | elnedyn22 24 | elnedyn22p 25 | 26 | [ martini ] 27 | BB SC1 28 | 29 | [ mapping ] 30 | charmm27 charmm36 31 | 32 | [ atoms ] 33 | 1 N !BB 34 | 2 HN !BB 35 | 3 CA BB 36 | 4 CB SC1 37 | 7 SG SC1 38 | 9 C !BB 39 | 10 O !BB 40 | 41 | [ chiral ] 42 | CB CA N C 43 | HB1 CA N C 44 | HB2 CA N C 45 | 46 | [ chiral ] 47 | HA CA N CB C ; L-Cys 48 | ; HA CA N C CB ; D-Cys 49 | -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/gln.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | GLN 17 | 18 | [from] 19 | universal 20 | 21 | [to] 22 | elnedyn21 23 | elnedyn22 24 | 25 | [ martini ] 26 | BB SC1 27 | 28 | [ mapping ] 29 | charmm27 charmm36 30 | 31 | [ atoms ] 32 | 1 N !BB 33 | 2 HN !BB 34 | 3 CA BB 35 | 4 CB SC1 36 | 5 CG SC1 37 | 6 CD SC1 38 | 7 OE1 SC1 39 | 8 NE2 SC1 40 | 9 HE21 SC1 41 | 10 HE22 SC1 42 | 11 C !BB 43 | 12 O !BB 44 | 45 | [ chiral ] 46 | CB CA N C 47 | HB1 CA N C 48 | HB2 CA N C 49 | 50 | [ chiral ] 51 | HA CA N CB C ; L-Gln 52 | ; HA CA N C CB ; D-Gln 53 | -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/gly.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | GLY 17 | 18 | [from] 19 | universal 20 | 21 | [to] 22 | elnedyn21 23 | elnedyn22 24 | elnedyn22p 25 | 26 | [ martini ] 27 | BB 28 | 29 | [ mapping ] 30 | charmm27 charmm36 31 | 32 | [ atoms ] 33 | 1 N !BB 34 | 2 HN !BB 35 | 3 CA BB 36 | 9 C !BB 37 | 10 O !BB 38 | -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/pro.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | PRO 17 | 18 | [from] 19 | universal 20 | 21 | [to] 22 | elnedyn21 23 | elnedyn22 24 | elnedyn22p 25 | 26 | [ martini ] 27 | BB SC1 28 | 29 | [ mapping ] 30 | charmm27 charmm36 31 | 32 | [ atoms ] 33 | 1 N !BB 34 | 2 CD SC1 35 | 3 CA BB 36 | 4 CB SC1 37 | 5 CG SC1 38 | 6 C !BB 39 | 7 O !BB 40 | 41 | [ chiral ] 42 | CB CA N C 43 | HB1 CA N C 44 | HB2 CA N C 45 | 46 | [ chiral ] 47 | HA CA N CB C ; L-Pro 48 | ; HA CA N C CB ; D-Pro 49 | -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/ser.charmm36.elnedyn22p.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | SER 17 | 18 | [from] 19 | universal 20 | 21 | [to] 22 | elnedyn22p 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N !BB 32 | 2 HN !BB 33 | 3 CA BB 34 | 5 CB SC1 35 | 8 OG SC1 36 | 9 HG1 SC1 37 | 10 C !BB 38 | 11 O !BB 39 | 40 | [ chiral ] 41 | CB CA N C 42 | HB1 CA N C 43 | HB2 CA N C 44 | 45 | [ chiral ] 46 | HA CA N CB C ; L-Ser 47 | ; HA CA N C CB ; D-Ser 48 | 49 | [ extra ] 50 | SCP SCN 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/ser.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | SER 17 | 18 | [from] 19 | universal 20 | 21 | [to] 22 | elnedyn21 23 | elnedyn22 24 | 25 | [ martini ] 26 | BB SC1 27 | 28 | [ mapping ] 29 | charmm27 charmm36 30 | 31 | [ atoms ] 32 | 1 N !BB 33 | 2 HN !BB 34 | 3 CA BB 35 | 5 CB SC1 36 | 8 OG SC1 37 | 9 HG1 SC1 38 | 10 C !BB 39 | 11 O !BB 40 | 41 | [ chiral ] 42 | CB CA N C 43 | HB1 CA N C 44 | HB2 CA N C 45 | 46 | [ chiral ] 47 | HA CA N CB C ; L-Ser 48 | ; HA CA N C CB ; D-Ser 49 | -------------------------------------------------------------------------------- /vermouth/data/mappings/elnedyn21/val.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | VAL 17 | 18 | [from] 19 | universal 20 | 21 | [to] 22 | elnedyn21 23 | elnedyn22 24 | elnedyn22p 25 | 26 | [ martini ] 27 | BB SC1 28 | 29 | [ mapping ] 30 | charmm27 charmm36 31 | 32 | [ atoms ] 33 | 1 N !BB 34 | 2 HN !BB 35 | 3 CA BB 36 | 5 CB SC1 37 | 8 CG1 SC1 38 | 12 CG2 SC1 39 | 16 C !BB 40 | 17 O !BB 41 | -------------------------------------------------------------------------------- /vermouth/data/mappings/fmn.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | FMN 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | FLA1 FLA2 FLA3 FLA4 FLA5 RIB1 RIB2 PO4 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 C9A FLA3 18 | 2 N10 FLA3 19 | 3 C10A FLA3 20 | 4 N1 FLA5 21 | 5 C2 FLA5 22 | 6 O2 FLA5 23 | 7 N3 FLA4 24 | 8 H3 !FLA4 25 | 9 C4 FLA4 26 | 10 O4 FLA4 27 | 11 C4A FLA2 28 | 12 N5 FLA2 29 | 13 C5A FLA2 30 | 14 C6 FLA2 31 | 15 C7 FLA1 32 | 16 CM7 FLA1 33 | 17 C8 FLA1 34 | 18 CM8 FLA1 35 | 19 C9 FLA3 36 | 20 CA RIB1 37 | 21 CB RIB1 38 | 22 OB RIB1 39 | 23 HB !RIB1 40 | 24 CG RIB1 RIB2 41 | 25 OG RIB1 RIB2 42 | 26 HG !RIB2 43 | 27 CD RIB2 44 | 28 OD RIB2 45 | 29 HD !RIB2 46 | 30 CE RIB2 47 | 31 OZ PO4 48 | 32 PH !PO4 49 | 33 OH PO4 50 | 34 HH !PO4 51 | 35 OT1 PO4 52 | 36 OT2 PO4 53 | -------------------------------------------------------------------------------- /vermouth/data/mappings/gln.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | GLN 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini22 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 CB SC1 35 | 5 CG SC1 36 | 6 CD SC1 37 | 7 OE1 SC1 38 | 8 NE2 SC1 39 | 9 HE21 SC1 40 | 10 HE22 SC1 41 | 11 C BB 42 | 12 O BB 43 | 44 | [ chiral ] 45 | CB CA N C 46 | HB1 CA N C 47 | HB2 CA N C 48 | 49 | [ chiral ] 50 | HA CA N CB C ; L-Gln 51 | ; HA CA N C CB ; D-Gln 52 | -------------------------------------------------------------------------------- /vermouth/data/mappings/gln.charmm36.martini22p.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | GLN 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini22p 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 CB SC1 35 | 5 CG SC1 36 | 6 CD SC1 37 | 7 OE1 SC1 38 | 8 NE2 SC1 39 | 9 HE21 SC1 40 | 10 HE22 SC1 41 | 11 C BB 42 | 12 O BB 43 | 44 | [ chiral ] 45 | CB CA N C 46 | HB1 CA N C 47 | HB2 CA N C 48 | 49 | [ chiral ] 50 | HA CA N CB C ; L-Gln 51 | ; HA CA N C CB ; D-Gln 52 | 53 | [ extra ] 54 | SCP SCN 55 | -------------------------------------------------------------------------------- /vermouth/data/mappings/gln.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | GLN 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB SC1 BB BB 21 | 5 CG SC1 SC1 BB 22 | 6 CD SC1 23 | 7 OE1 SC1 24 | 8 NE2 SC1 25 | 9 HE21 SC1 26 | 10 HE22 SC1 27 | 11 C BB 28 | 12 O BB 29 | 30 | -------------------------------------------------------------------------------- /vermouth/data/mappings/glu.gromos.map: -------------------------------------------------------------------------------- 1 | ;24.1.13 kri added protonated form 2 | 3 | [ molecule ] 4 | GLU 5 | 6 | [from] 7 | gromos 8 | 9 | [to] 10 | martini22 11 | 12 | [ martini ] 13 | BB SC1 14 | 15 | [ mapping ] 16 | gromos 17 | 18 | [ atoms ] 19 | 1 N BB 20 | 2 H BB 21 | 3 CA BB 22 | 4 CB SC1 BB BB 23 | 5 CG SC1 SC1 BB 24 | 6 CD SC1 25 | 7 OE1 SC1 26 | 8 OE2 SC1 27 | 9 C BB 28 | 10 O BB 29 | -------------------------------------------------------------------------------- /vermouth/data/mappings/glu0.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | GLU0 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB SC1 BB BB 21 | 5 CG SC1 SC1 BB 22 | 6 CD SC1 23 | 7 OE1 SC1 24 | 8 OE2 SC1 25 | 9 HE2 SC1 26 | 10 C BB 27 | 11 O BB 28 | 29 | -------------------------------------------------------------------------------- /vermouth/data/mappings/gly.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | GLY 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini22 23 | martini22p 24 | 25 | [ martini ] 26 | BB 27 | 28 | [ mapping ] 29 | charmm27 charmm36 30 | 31 | [ atoms ] 32 | 1 N BB 33 | 2 HN BB 34 | 3 CA BB 35 | 9 C BB 36 | 10 O BB 37 | -------------------------------------------------------------------------------- /vermouth/data/mappings/gly.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | GLY 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 C BB 21 | 5 O BB 22 | 23 | -------------------------------------------------------------------------------- /vermouth/data/mappings/his.charmm.mapping: -------------------------------------------------------------------------------- 1 | [ block ] 2 | [ from ] 3 | charmm 4 | [ to ] 5 | martini22 6 | 7 | [ from blocks ] 8 | HIS 9 | 10 | [ to blocks ] 11 | HSE 12 | 13 | [ mapping ] 14 | N BB 15 | HN BB 16 | CA BB 17 | HA BB 18 | CB SC1 19 | HB1 SC1 20 | HB2 SC1 21 | CD2 SC2 22 | HD2 SC2 23 | CG SC1 24 | NE2 SC2 25 | HE2 SC2 26 | ND1 SC3 27 | CE1 SC3 28 | HE1 SC3 29 | C BB 30 | O BB -------------------------------------------------------------------------------- /vermouth/data/mappings/his.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | HIS 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 SC2 SC3 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB SC1 BB 21 | 5 CG SC1 22 | 6 ND1 SC3 SC1 23 | 7 CD2 SC2 SC1 24 | 8 CE1 SC3 SC3 SC2 25 | 9 NE2 SC2 SC2 SC3 26 | 10 HE2 SC2 27 | 11 C BB 28 | 12 O BB 29 | 30 | [ chiral ] 31 | CB CA N C 32 | 33 | -------------------------------------------------------------------------------- /vermouth/data/mappings/his.gromos.mapping: -------------------------------------------------------------------------------- 1 | [ block ] 2 | [ from ] 3 | gromos 4 | [ to ] 5 | martini22 6 | 7 | [ from blocks ] 8 | HIS 9 | 10 | [ to blocks ] 11 | HSE 12 | 13 | [ mapping ] 14 | N BB 15 | H BB 16 | CA BB 17 | CB SC1 18 | CG SC1 19 | ND1 SC3 20 | HD1 SC3 21 | CD2 SC2 22 | HD2 SC2 23 | CE1 SC3 24 | HE1 SC3 25 | NE2 SC2 26 | C BB 27 | O BB 28 | -------------------------------------------------------------------------------- /vermouth/data/mappings/ile.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | ILE 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB SC1 BB BB 21 | 5 CG1 SC1 SC1 BB 22 | 6 CG2 SC1 SC1 BB 23 | 7 CD SC1 24 | 8 C BB 25 | 9 O BB 26 | 27 | -------------------------------------------------------------------------------- /vermouth/data/mappings/leu.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | LEU 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB SC1 BB BB 21 | 5 CG SC1 SC1 BB 22 | 6 CD1 SC1 23 | 7 CD2 SC1 24 | 8 C BB 25 | 9 O BB 26 | 27 | -------------------------------------------------------------------------------- /vermouth/data/mappings/lys.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | LYS 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 SC2 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB SC1 BB BB 21 | 5 CG SC1 SC1 BB 22 | 6 CD SC1 23 | 7 CE SC1 SC1 SC2 24 | 8 NZ SC2 SC2 SC1 25 | 9 HZ1 SC2 26 | 10 HZ2 SC2 27 | 11 HZ3 SC2 28 | 12 C BB 29 | 13 O BB 30 | 31 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/ala.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ALA 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3001 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | amber27 amber36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 HB3 !SC1 39 | 9 C BB 40 | 10 O BB 41 | 42 | [ chiral ] 43 | CB CA N C 44 | HB1 CA N C 45 | HB2 CA N C 46 | HB3 CA N C 47 | 48 | [ chiral ] 49 | HA CA N CB C ; L-Ala 50 | ; HA CA N C CB ; D-Ala 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/ala.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ALA 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini3001 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 HB3 !SC1 39 | 9 C BB 40 | 10 O BB 41 | 42 | [ chiral ] 43 | CB CA N C 44 | HB1 CA N C 45 | HB2 CA N C 46 | HB3 CA N C 47 | 48 | [ chiral ] 49 | HA CA N CB C ; L-Ala 50 | ; HA CA N C CB ; D-Ala 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/antr.charmm36.map: -------------------------------------------------------------------------------- 1 | ; ANTH 2 | [ molecule ] 3 | ANTR 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R4 R1 R6 R5 R2 R3 R7 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C3 R1 19 | 2 C2 R1 20 | 3 C1 R3 21 | 4 C14 R3 22 | 5 C13 R4 23 | 6 C12 R6 24 | 7 C11 R6 25 | 8 C10 R7 26 | 9 C9 R7 27 | 10 C8 R5 28 | 11 C7 R5 29 | 12 C6 R4 30 | 13 C5 R2 31 | 14 C4 R2 32 | 15 H3 R1 33 | 16 H2 R1 34 | 17 H1 R3 35 | 18 H13 R4 36 | 19 H11 R6 37 | 20 H10 R7 38 | 21 H9 R7 39 | 22 H8 R5 40 | 23 H6 R4 41 | 24 H4 R2 42 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/ash.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ASH 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3001 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | amber 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 CG SC1 39 | 9 OD1 SC1 40 | 10 OD2 SC1 41 | 11 HD2 !SC1 42 | 12 C BB 43 | 13 O BB 44 | 45 | [ chiral ] 46 | CB CA N C 47 | HB1 CA N C 48 | HB2 CA N C 49 | 50 | [ chiral ] 51 | HA CA N CB C ; L-Asp 52 | ; HA CA N C CB ; D-Asp 53 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/asp.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ASP 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3001 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | amber27 amber36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 CG SC1 39 | 9 OD1 SC1 40 | 10 OD2 SC1 41 | 11 HD2 !SC1 42 | 12 C BB 43 | 13 O BB 44 | 45 | [ chiral ] 46 | CB CA N C 47 | HB1 CA N C 48 | HB2 CA N C 49 | 50 | [ chiral ] 51 | HA CA N CB C ; L-Asp 52 | ; HA CA N C CB ; D-Asp 53 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/asp.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ASP 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini3001 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 CG SC1 39 | 9 OD1 SC1 40 | 10 OD2 SC1 41 | 11 HD2 !SC1 42 | 12 C BB 43 | 13 O BB 44 | 45 | [ chiral ] 46 | CB CA N C 47 | HB1 CA N C 48 | HB2 CA N C 49 | 50 | [ chiral ] 51 | HA CA N CB C ; L-Asp 52 | ; HA CA N C CB ; D-Asp 53 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/aspp.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ASPP 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini3001 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 CG SC1 39 | 9 OD1 SC1 40 | 10 OD2 SC1 41 | 11 HD2 !SC1 42 | 12 C BB 43 | 13 O BB 44 | 45 | [ chiral ] 46 | CB CA N C 47 | HB1 CA N C 48 | HB2 CA N C 49 | 50 | [ chiral ] 51 | HA CA N CB C ; L-Asp 52 | ; HA CA N C CB ; D-Asp 53 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/bald.charmm36.map: -------------------------------------------------------------------------------- 1 | ; BEAL 2 | [ molecule ] 3 | BALD 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R3 R2 R4 O1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 O O1 19 | 2 C O1 20 | 3 CG R2 R3 21 | 4 CD1 R2 22 | 5 CE1 R2 R4 23 | 6 CZ R4 24 | 7 CE2 R3 R4 25 | 8 CD2 R3 26 | 9 HA O1 27 | 10 HD1 R2 28 | 11 HZ R4 29 | 12 HD2 R3 30 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/benz.charmm36.map: -------------------------------------------------------------------------------- 1 | ; BENZ 2 | [ molecule ] 3 | BENZ 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R2 R3 R1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 CG R3 19 | 2 CD1 R1 20 | 3 CE1 R1 21 | 4 CZ R2 22 | 5 CE2 R2 23 | 6 CD2 R3 24 | 7 HG R3 25 | 8 HD1 R1 26 | 9 HE1 R1 27 | 10 HZ R2 28 | 11 HE2 R2 29 | 12 HD2 R3 30 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/c3.charmm36.map: -------------------------------------------------------------------------------- 1 | ; CPR 2 | [ molecule ] 3 | C3 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C1 R1 19 | 2 C2 R1 20 | 3 C3 R1 21 | 4 H11 R1 22 | 5 H12 R1 23 | 6 H21 R1 24 | 7 H22 R1 25 | 8 H32 R1 26 | 9 H31 R1 27 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/chxe.charmm36.map: -------------------------------------------------------------------------------- 1 | ; CHEXE 2 | [ molecule ] 3 | CHXE 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | C1 C2 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C3 C2 19 | 2 C2 C2 20 | 3 C1 C2 21 | 4 C6 C1 22 | 5 C5 C1 23 | 6 C4 C1 24 | 7 H31 C2 25 | 8 H32 C2 26 | 9 H21 C2 27 | 10 H22 C2 28 | 11 H12 C2 29 | 12 H11 C2 30 | 13 H6 C1 31 | 14 H5 C1 32 | 15 H41 C1 33 | 16 H42 C1 34 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/cpen.charmm36.map: -------------------------------------------------------------------------------- 1 | ; CYPE 2 | [ molecule ] 3 | CPEN 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | C1 C2 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C1 C2 19 | 2 C2 C1 20 | 3 C3 C1 21 | 4 C4 C2 22 | 5 C5 C2 23 | 6 H11 C2 24 | 7 H12 C2 25 | 8 H22 C1 26 | 9 H21 C1 27 | 10 H31 C1 28 | 11 H32 C1 29 | 12 H41 C2 30 | 13 H42 C2 31 | 14 H51 C2 32 | 15 H52 C2 33 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/cume.charmm36.map: -------------------------------------------------------------------------------- 1 | ; CUME 2 | [ molecule ] 3 | CUME 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R2 R1 R4 R3 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C3 R1 19 | 2 C4 R1 20 | 3 C5 R1 21 | 4 CA4 R2 R3 22 | 5 CA3 R2 23 | 6 CA2 R2 R4 24 | 7 CA1 R4 25 | 8 CA6 R3 R4 26 | 9 CA5 R3 27 | 10 H32 R1 28 | 11 H33 R1 29 | 12 H31 R1 30 | 13 H41 R1 31 | 14 H51 R1 32 | 15 H52 R1 33 | 16 H53 R1 34 | 17 HA3 R2 35 | 18 HA1 R4 36 | 19 HA5 R3 37 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/cys.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | CYS 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3001 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | amber27 amber36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 SG SC1 39 | 9 HG1 !SC1 40 | 10 C BB 41 | 11 O BB 42 | 43 | [ chiral ] 44 | CB CA N C 45 | HB1 CA N C 46 | HB2 CA N C 47 | 48 | [ chiral ] 49 | HA CA N CB C ; L-Cys 50 | ; HA CA N C CB ; D-Cys 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/cys.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | CYS 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini3001 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 SG SC1 39 | 9 HG1 !SC1 40 | 10 C BB 41 | 11 O BB 42 | 43 | [ chiral ] 44 | CB CA N C 45 | HB1 CA N C 46 | HB2 CA N C 47 | 48 | [ chiral ] 49 | HA CA N CB C ; L-Cys 50 | ; HA CA N C CB ; D-Cys 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/cysf.map: -------------------------------------------------------------------------------- 1 | ; CHARMM36m -> Martini 3 mapping for cysteine farnesyl 2 | ; Original manuscript: 3 | ; 4 | 5 | [ molecule ] 6 | CYSF 7 | 8 | [ from ] 9 | charmm 10 | 11 | [ to ] 12 | martini3001 13 | 14 | [ martini ] 15 | BB SC1 C1 C2 C3 C4 C5 C6 16 | 17 | [ mapping ] 18 | charmm36m 19 | 20 | [ atoms ] 21 | 1 N BB 22 | 2 HN BB 23 | 3 CA BB 24 | 4 HA BB 25 | 5 C BB 26 | 6 O BB 27 | 7 CB SC1 28 | 8 HB1 SC1 29 | 9 HB2 SC1 30 | 10 SG SC1 31 | 11 C1 C1 32 | 12 H1A C1 33 | 13 H1B C1 34 | 14 C2 C1 35 | 15 H2A C1 36 | 16 C3 C4 37 | 17 C4 C4 38 | 18 H4A C4 39 | 19 H4B C4 40 | 20 H4C C4 41 | 21 C5 C1 42 | 22 H5A C1 43 | 23 H5B C1 44 | 24 C6 C2 45 | 25 H6A C2 46 | 26 H6B C2 47 | 27 C7 C2 48 | 28 H7A C2 49 | 29 C8 C5 50 | 30 C9 C5 51 | 31 H9A C5 52 | 32 H9B C5 53 | 33 H9C C5 54 | 34 C10 C2 55 | 35 H10A C2 56 | 36 H10B C2 57 | 37 C11 C3 58 | 38 H11A C3 59 | 39 H11B C3 60 | 40 C12 C3 61 | 41 H12A C3 62 | 42 C13 C6 63 | 43 C14 C3 64 | 44 H14A C3 65 | 45 H14B C3 66 | 46 H14C C3 67 | 47 C15 C6 68 | 48 H15A C6 69 | 49 H15B C6 70 | 50 H15C C6 71 | 72 | [ chiral ] 73 | CB CA N C 74 | HB1 CA N C 75 | HB2 CA N C 76 | 77 | [ chiral ] 78 | HA CA N CB C ; L-Cys 79 | ; HA CA N C CB ; D-Cys 80 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/diol.charmm36.map: -------------------------------------------------------------------------------- 1 | ; DXLA 2 | [ molecule ] 3 | DIOL 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | O2 O1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 O1 O2 19 | 2 C5 O1 20 | 3 C4 O1 21 | 4 O3 O2 22 | 5 C2 O2 23 | 6 H51 O1 24 | 7 H52 O1 25 | 8 H42 O1 26 | 9 H41 O1 27 | 10 H22 O2 28 | 11 H21 O2 29 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/diox.charmm36.map: -------------------------------------------------------------------------------- 1 | ; DIOX 2 | [ molecule ] 3 | DIOX 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | O2 O1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 O1 O2 19 | 2 C2 O2 20 | 3 C3 O1 21 | 4 O4 O1 22 | 5 C5 O1 23 | 6 C6 O2 24 | 7 H21 O2 25 | 8 H22 O2 26 | 9 H31 O1 27 | 10 H32 O1 28 | 11 H51 O1 29 | 12 H52 O1 30 | 13 H61 O2 31 | 14 H62 O2 32 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/dman.charmm36.map: -------------------------------------------------------------------------------- 1 | ; DMAN 2 | [ molecule ] 3 | DMAN 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R3 R2 R4 N1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C7 N1 19 | 2 N1 N1 20 | 3 C8 N1 21 | 4 C6 R2 R3 22 | 5 C1 R3 23 | 6 C2 R3 R4 24 | 7 C3 R4 25 | 8 C4 R2 R4 26 | 9 C5 R2 27 | 10 H72 N1 28 | 11 H73 N1 29 | 12 H71 N1 30 | 13 H81 N1 31 | 14 H82 N1 32 | 15 H83 N1 33 | 16 H1 R3 34 | 17 H3 R4 35 | 18 H5 R2 36 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/eben.charmm36.map: -------------------------------------------------------------------------------- 1 | ; EBEN 2 | [ molecule ] 3 | EBEN 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R3 R2 R4 R1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 CA R4 19 | 2 CB R4 20 | 3 CG R2 R3 21 | 4 CD1 R2 22 | 5 CE1 R1 R2 23 | 6 CZ R1 24 | 7 CE2 R1 R3 25 | 8 CD2 R3 26 | 9 HA1 R4 27 | 10 HA2 R4 28 | 11 HA3 R4 29 | 12 HB1 R4 30 | 13 HB2 R4 31 | 14 HD1 R2 32 | 15 HZ R1 33 | 16 HD2 R3 34 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/fura.charmm36.map: -------------------------------------------------------------------------------- 1 | ; FURA 2 | [ molecule ] 3 | FURA 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R2 R3 O1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C3 R3 19 | 2 C2 R2 20 | 3 C1 R2 21 | 4 O5 O1 22 | 5 C4 R3 23 | 6 H3 R3 24 | 7 H2 R2 25 | 8 H1 R2 26 | 9 H4 R3 27 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/gly.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | GLY 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3001 23 | 24 | [ martini ] 25 | BB 26 | 27 | [ mapping ] 28 | amber27 amber36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA1 !BB 35 | 5 HA2 !BB 36 | 9 C BB 37 | 10 O BB 38 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/gly.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | GLY 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini3001 23 | 24 | [ martini ] 25 | BB 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA1 !BB 35 | 5 HA2 !BB 36 | 9 C BB 37 | 10 O BB 38 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/glym.map: -------------------------------------------------------------------------------- 1 | ; CHARMM36m -> Martini 3 mapping for glycine myristoyl 2 | ; Original manuscript: 3 | ; 4 | 5 | [ molecule ] 6 | GLYM 7 | 8 | [ from ] 9 | charmm 10 | 11 | [ to ] 12 | martini3001 13 | 14 | [ martini ] 15 | BB C1 C2 C3 C4 16 | 17 | [ mapping ] 18 | charmm36m 19 | 20 | [ atoms ] 21 | 1 N BB 22 | 2 HN BB 23 | 3 CA BB 24 | 4 HA1 BB 25 | 5 HA2 BB 26 | 6 C BB 27 | 7 O BB 28 | 8 C1 C1 29 | 9 O1 C1 30 | 10 C2 C1 31 | 11 H2A C1 32 | 12 H2B C1 33 | 13 C3 C2 34 | 14 H3A C2 35 | 15 H3B C2 36 | 16 C4 C2 37 | 17 H4A C2 38 | 18 H4B C2 39 | 19 C5 C2 40 | 20 H5A C2 41 | 21 H5B C2 42 | 22 C6 C2 43 | 23 H6A C2 44 | 24 H6B C2 45 | 25 C7 C3 46 | 26 H7A C3 47 | 27 H7B C3 48 | 28 C8 C3 49 | 29 H8A C3 50 | 30 H8B C3 51 | 31 C9 C3 52 | 32 H9A C3 53 | 33 H9B C3 54 | 34 C10 C3 55 | 35 H10A C3 56 | 36 H10B C3 57 | 37 C11 C4 58 | 38 H11A C4 59 | 39 H11B C4 60 | 40 C12 C4 61 | 41 H12A C4 62 | 42 H12B C4 63 | 43 C13 C4 64 | 44 H13A C4 65 | 45 H13B C4 66 | 46 C14 C4 67 | 47 H14A C4 68 | 48 H14B C4 69 | 49 H14C C4 70 | 71 | [ chiral ] 72 | CB CA N C 73 | HB1 CA N C 74 | HB2 CA N C 75 | 76 | [ chiral ] 77 | HA CA N CB C ; L-Cys 78 | ; HA CA N C CB ; D-Cys 79 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/hid.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | HID 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3001 23 | 24 | [ martini ] 25 | BB SC1 SC2 SC3 26 | 27 | [ mapping ] 28 | amber 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 H BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 CG SC2 39 | 9 ND1 SC2 40 | 10 HD1 SC1 41 | 11 CE1 SC2 42 | 12 HE1 SC2 43 | 13 NE2 SC3 44 | 14 CD2 SC3 45 | 15 HD2 SC3 46 | 16 C BB 47 | 17 O BB 48 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/his.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | HIS 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3001 23 | 24 | [ martini ] 25 | BB SC1 SC2 SC3 26 | 27 | [ mapping ] 28 | amber27 amber36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 CD2 SC2 39 | 9 HD2 SC2 40 | 10 CG SC1 41 | 11 NE2 SC2 42 | 12 HE2 SC2 43 | 13 ND1 SC3 44 | 14 CE1 SC3 45 | 15 C BB 46 | 16 O BB 47 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/imia.charmm36.map: -------------------------------------------------------------------------------- 1 | ; IMID 2 | [ molecule ] 3 | IMIA 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R3 N2 N1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 CG R3 19 | 2 CD2 R3 20 | 3 NE2 N1 21 | 4 CE1 N2 22 | 5 ND1 N2 23 | 6 HD1 N2 24 | 7 HG R3 25 | 8 HD2 R3 26 | 9 HE1 N2 27 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/inda.charmm36.map: -------------------------------------------------------------------------------- 1 | ; INDA 2 | [ molecule ] 3 | INDA 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | N4 R1 N5 R2 R3 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C6 R1 19 | 2 C7 R2 20 | 3 C8 R2 21 | 4 C9 R3 22 | 5 N1 N5 23 | 6 H1 N5 24 | 7 N2 N4 N5 25 | 8 C3 N4 26 | 9 C4 R3 27 | 10 C5 R1 28 | 11 H6 R1 29 | 12 H7 R2 30 | 13 H8 R2 31 | 14 H3 N4 32 | 15 H5 R1 33 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/indo.charmm36.map: -------------------------------------------------------------------------------- 1 | ; INDO 2 | [ molecule ] 3 | INDO 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R4 R1 N5 R2 R3 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 CE2 R3 19 | 2 CD2 R3 20 | 3 CG R4 21 | 4 CD1 R4 N5 22 | 5 NE1 N5 23 | 6 CE3 R1 24 | 7 CZ3 R1 25 | 8 CH2 R2 26 | 9 CZ2 R2 27 | 10 HG R4 28 | 11 HE1 N5 29 | 12 HE3 R1 30 | 13 HZ3 R1 31 | 14 HH2 R2 32 | 15 HZ2 R2 33 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/mboa.charmm36.map: -------------------------------------------------------------------------------- 1 | ; MBZOA 2 | [ molecule ] 3 | MBOA 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R3 R2 R4 O1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C8 O1 19 | 2 O8 O1 20 | 3 C7 O1 21 | 4 O7 O1 22 | 5 C1 R2 R3 23 | 6 C2 R2 24 | 7 C3 R2 R4 25 | 8 C4 R4 26 | 9 C5 R3 R4 27 | 10 C6 R3 28 | 11 H81 O1 29 | 12 H82 O1 30 | 13 H83 O1 31 | 14 H2 R2 32 | 15 H4 R4 33 | 16 H6 R3 34 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/mcpe.charmm36.map: -------------------------------------------------------------------------------- 1 | ; MCYPE 2 | [ molecule ] 3 | MCPE 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | C1 C2 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C6 C1 19 | 2 C5 C1 20 | 3 C1 C1 21 | 4 C2 C2 22 | 5 C3 C2 23 | 6 C4 C1 24 | 7 H62 C1 25 | 8 H63 C1 26 | 9 H61 C1 27 | 10 H51 C1 28 | 11 H22 C2 29 | 12 H21 C2 30 | 13 H31 C2 31 | 14 H32 C2 32 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/meob.charmm36.map: -------------------------------------------------------------------------------- 1 | ; XBZ 2 | [ molecule ] 3 | MEOB 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R3 R2 R4 O1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 CM O1 19 | 2 OZ O1 20 | 3 CZ R2 R3 21 | 4 CE1 R3 22 | 5 CD1 R3 R4 23 | 6 CG R4 24 | 7 CD2 R2 R4 25 | 8 CE2 R2 26 | 9 HM1 O1 27 | 10 HM2 O1 28 | 11 HM3 O1 29 | 12 HE1 R3 30 | 13 HG R4 31 | 14 HE2 R2 32 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/mind.charmm36.map: -------------------------------------------------------------------------------- 1 | ; MIND 2 | [ molecule ] 3 | MIND 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R4 R1 N5 R2 R3 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 CE3 R1 19 | 2 CZ3 R1 20 | 3 CH2 R2 21 | 4 CZ2 R2 22 | 5 CE2 R3 23 | 6 CD2 R3 24 | 7 CG R4 25 | 8 CD1 N5 26 | 9 NE1 N5 27 | 10 HE1 N5 28 | 11 CB R4 29 | 12 HE3 R1 30 | 13 HZ3 R1 31 | 14 HH2 R2 32 | 15 HZ2 R2 33 | 16 HD1 N5 34 | 17 HB1 R4 35 | 18 HB2 R4 36 | 19 HB3 R4 37 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/mxyl.charmm36.map: -------------------------------------------------------------------------------- 1 | ; MXYLE 2 | [ molecule ] 3 | MXYL 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R3 R1 R2 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C2 R1 19 | 2 CD2 R1 20 | 3 CG R1 21 | 4 CD1 R3 22 | 5 CE1 R3 23 | 6 CZ R2 24 | 7 CE2 R2 25 | 8 C1 R2 26 | 9 H21 R1 27 | 10 H22 R1 28 | 11 H23 R1 29 | 12 HG R1 30 | 13 HD1 R3 31 | 14 HE1 R3 32 | 15 HE2 R2 33 | 16 H13 R2 34 | 17 H11 R2 35 | 18 H12 R2 36 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/naft.charmm36.map: -------------------------------------------------------------------------------- 1 | ; NAPH 2 | [ molecule ] 3 | NAFT 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R4 R1 R5 R2 R3 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C3 R2 19 | 2 C2 R1 20 | 3 C1 R1 21 | 4 C10 R3 22 | 5 C9 R4 23 | 6 C8 R4 24 | 7 C7 R5 25 | 8 C6 R5 26 | 9 C5 R3 27 | 10 C4 R2 28 | 11 H3 R2 29 | 12 H2 R1 30 | 13 H1 R1 31 | 14 H9 R4 32 | 15 H8 R4 33 | 16 H7 R5 34 | 17 H6 R5 35 | 18 H4 R2 36 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/nitb.charmm36.map: -------------------------------------------------------------------------------- 1 | ; NIBZ 2 | [ molecule ] 3 | NITB 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R2 R3 R4 N1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C3 R4 19 | 2 C2 R3 R4 20 | 3 C1 R3 21 | 4 C6 R2 R3 22 | 5 C5 R2 23 | 6 C4 R2 R4 24 | 7 N6 N1 25 | 8 O6B N1 26 | 9 O6A N1 27 | 10 H3 R4 28 | 11 H1 R3 29 | 12 H5 R2 30 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/oxyl.charmm36.map: -------------------------------------------------------------------------------- 1 | ; OXYLE 2 | [ molecule ] 3 | OXYL 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R3 R2 R1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C1 R2 19 | 2 CZ R2 20 | 3 CE2 R1 21 | 4 C2 R1 22 | 5 CD2 R1 23 | 6 CG R3 24 | 7 CD1 R3 25 | 8 CE1 R2 26 | 9 H11 R2 27 | 10 H12 R2 28 | 11 H13 R2 29 | 12 H21 R1 30 | 13 H22 R1 31 | 14 H23 R1 32 | 15 HD2 R1 33 | 16 HG R3 34 | 17 HD1 R3 35 | 18 HE1 R2 36 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/pcro.charmm36.map: -------------------------------------------------------------------------------- 1 | ; PCRE 2 | [ molecule ] 3 | PCRO 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R3 R2 R4 P1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C1 R4 19 | 2 CZ R4 20 | 3 CE1 R2 21 | 4 CD1 R2 22 | 5 CG P1 23 | 6 O2 P1 24 | 7 CD2 R3 25 | 8 CE2 R3 26 | 9 H11 R4 27 | 10 H12 R4 28 | 11 H13 R4 29 | 12 HE1 R2 30 | 13 HD1 R2 31 | 14 H2 P1 32 | 15 HD2 R3 33 | 16 HE2 R3 34 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/phen.charmm36.map: -------------------------------------------------------------------------------- 1 | ; PHEN 2 | [ molecule ] 3 | PHEN 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R3 R2 O1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 CG R2 R3 19 | 2 CD1 R2 20 | 3 CE1 O1 R2 21 | 4 CZ O1 22 | 5 CE2 O1 R3 23 | 6 CD2 R3 24 | 7 OH O1 25 | 8 HD1 R2 26 | 9 HD2 R3 27 | 10 HH O1 28 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/phmk.charmm36.map: -------------------------------------------------------------------------------- 1 | ; ACPH 2 | [ molecule ] 3 | PHMK 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R2 R1 R4 R3 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C1 R1 19 | 2 C2 R1 20 | 3 O2 R1 21 | 4 C3 R2 R3 22 | 5 C8 R2 23 | 6 C7 R2 R4 24 | 7 C6 R4 25 | 8 C5 R3 R4 26 | 9 C4 R3 27 | 10 H13 R1 28 | 11 H11 R1 29 | 12 H12 R1 30 | 13 H8 R2 31 | 14 H6 R4 32 | 15 H4 R3 33 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/prld.charmm36.map: -------------------------------------------------------------------------------- 1 | ; PYLI 2 | [ molecule ] 3 | PRLD 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R2 N1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C4 R2 19 | 2 C3 R2 20 | 3 C2 N1 R2 21 | 4 N1 N1 22 | 5 C5 N1 R2 23 | 6 H41 R2 24 | 7 H42 R2 25 | 8 H32 R2 26 | 9 H31 R2 27 | 10 H1 N1 28 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/pxyl.charmm36.map: -------------------------------------------------------------------------------- 1 | ; PXYLE 2 | [ molecule ] 3 | PXYL 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R2 R1 R4 R3 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C2 R1 19 | 2 CG R1 20 | 3 CD1 R2 21 | 4 CE1 R2 22 | 5 CZ R4 23 | 6 C1 R4 24 | 7 CE2 R3 25 | 8 CD2 R3 26 | 9 H21 R1 27 | 10 H22 R1 28 | 11 H23 R1 29 | 12 HD1 R2 30 | 13 HE1 R2 31 | 14 H11 R4 32 | 15 H12 R4 33 | 16 H13 R4 34 | 17 HE2 R3 35 | 18 HD2 R3 36 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/pyr1.charmm36.map: -------------------------------------------------------------------------------- 1 | ; PYRI 2 | [ molecule ] 3 | PYR1 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R3 R2 N1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C4 R2 19 | 2 C3 R2 20 | 3 C2 N1 21 | 4 N1 N1 22 | 5 C6 R3 23 | 6 C5 R3 24 | 7 H4 R2 25 | 8 H3 R2 26 | 9 H2 N1 27 | 10 H6 R3 28 | 11 H5 R3 29 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/pyrd.charmm36.map: -------------------------------------------------------------------------------- 1 | ; PYAZ 2 | [ molecule ] 3 | PYRD 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R2 NN R3 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C4 R3 19 | 2 C5 R2 20 | 3 C6 R2 21 | 4 N1 NN 22 | 5 N2 NN 23 | 6 C3 R3 24 | 7 H4 R3 25 | 8 H5 R2 26 | 9 H6 R2 27 | 10 H3 R3 28 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/pyrl.charmm36.map: -------------------------------------------------------------------------------- 1 | ; PYRR 2 | [ molecule ] 3 | PYRL 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R3 R2 N1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 N5 N1 19 | 2 H5 N1 20 | 3 C1 R2 21 | 4 C2 R2 22 | 5 C3 R3 23 | 6 C4 R3 24 | 7 H1 R2 25 | 8 H2 R2 26 | 9 H3 R3 27 | 10 H4 R3 28 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/pyrm.charmm36.map: -------------------------------------------------------------------------------- 1 | ; PYMI 2 | [ molecule ] 3 | PYRM 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R3 N2 N1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C5 R3 19 | 2 C6 R3 20 | 3 N1 N1 21 | 4 C2 N1 22 | 5 N3 N2 23 | 6 C4 N2 24 | 7 H5 R3 25 | 8 H6 R3 26 | 9 H2 N1 27 | 10 H4 N2 28 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/qinl.charmm36.map: -------------------------------------------------------------------------------- 1 | ; QUIN 2 | [ molecule ] 3 | QINL 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R4 R5 R2 R3 N1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 N1 N1 19 | 2 C2 N1 20 | 3 C3 R2 21 | 4 C4 R2 22 | 5 C5 R3 23 | 6 C6 R5 24 | 7 C7 R5 25 | 8 C8 R4 26 | 9 C9 R4 27 | 10 C10 R3 28 | 11 H2 N1 29 | 12 H3 R2 30 | 13 H4 R2 31 | 14 H6 R5 32 | 15 H7 R5 33 | 16 H8 R4 34 | 17 H9 R4 35 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/ser.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | SER 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3001 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | amber27 amber36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 OG SC1 39 | 9 HG1 SC1 40 | 10 C BB 41 | 11 O BB 42 | 43 | [ chiral ] 44 | CB CA N C 45 | HB1 CA N C 46 | HB2 CA N C 47 | 48 | [ chiral ] 49 | HA CA N CB C ; L-Ser 50 | ; HA CA N C CB ; D-Ser 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/ser.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | SER 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini3001 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 OG SC1 39 | 9 HG1 SC1 40 | 10 C BB 41 | 11 O BB 42 | 43 | [ chiral ] 44 | CB CA N C 45 | HB1 CA N C 46 | HB2 CA N C 47 | 48 | [ chiral ] 49 | HA CA N CB C ; L-Ser 50 | ; HA CA N C CB ; D-Ser 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/sm139.charmm36.map: -------------------------------------------------------------------------------- 1 | ; 2NITL 2 | [ molecule ] 3 | SM139 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R3 R2 R4 N1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 CA R2 19 | 2 CG R2 20 | 3 CD1 R2 R4 21 | 4 CE1 R4 22 | 5 CZ R3 R4 23 | 6 CE2 R3 24 | 7 CD2 R2 R3 25 | 8 N1 N1 26 | 9 O1 N1 27 | 10 O2 N1 28 | 11 HA3 R2 29 | 12 HA2 R2 30 | 13 HA R2 31 | 14 HE1 R4 32 | 15 HE2 R3 33 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/styr.charmm36.map: -------------------------------------------------------------------------------- 1 | ; STYR 2 | [ molecule ] 3 | STYR 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R3 R2 R4 R1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 CE1 R2 19 | 2 CD1 R2 R4 20 | 3 CG R4 21 | 4 CD2 R3 R4 22 | 5 CE2 R3 23 | 6 CZ R2 R3 24 | 7 C1 R1 25 | 8 C2 R1 26 | 9 HE1 R2 27 | 10 HG R4 28 | 11 HE2 R3 29 | 12 H1 R1 30 | 13 H21 R1 31 | 14 H22 R1 32 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/thaz.charmm36.map: -------------------------------------------------------------------------------- 1 | ; THAZ 2 | [ molecule ] 3 | THAZ 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R2 R3 N1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 N3 N1 19 | 2 C2 R3 20 | 3 C1 R3 21 | 4 S5 R2 22 | 5 C4 N1 23 | 6 H2 R3 24 | 7 H1 R3 25 | 8 H4 N1 26 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/thf.charmm36.map: -------------------------------------------------------------------------------- 1 | ; THF 2 | [ molecule ] 3 | THF 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R2 O1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C2' R2 19 | 2 C3' R2 20 | 3 C4' O1 R2 21 | 4 O4' O1 22 | 5 C1' O1 R2 23 | 6 H21' R2 24 | 7 H22' R2 25 | 8 H31' R2 26 | 9 H32' R2 27 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/thip.charmm36.map: -------------------------------------------------------------------------------- 1 | ; THIO 2 | [ molecule ] 3 | THIP 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R2 R3 S1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C3 R3 19 | 2 C2 R2 20 | 3 C1 R2 21 | 4 S5 S1 22 | 5 C4 R3 23 | 6 H3 R3 24 | 7 H2 R2 25 | 8 H1 R2 26 | 9 H4 R3 27 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/thp.charmm36.map: -------------------------------------------------------------------------------- 1 | ; THP 2 | [ molecule ] 3 | THP 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R2 O1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 O1 O1 19 | 2 C2 O1 20 | 3 C3 R2 21 | 4 C4 R2 22 | 5 C5 R2 23 | 6 C6 O1 24 | 7 H21 O1 25 | 8 H22 O1 26 | 9 H31 R2 27 | 10 H32 R2 28 | 11 H41 R2 29 | 12 H42 R2 30 | 13 H51 R2 31 | 14 H52 R2 32 | 15 H61 O1 33 | 16 H62 O1 34 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/tolu.charmm36.map: -------------------------------------------------------------------------------- 1 | ; TOLU 2 | [ molecule ] 3 | TOLU 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R2 R1 R3 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 CT R1 19 | 2 CZ R1 20 | 3 CE1 R1 R2 21 | 4 CD1 R2 22 | 5 CG R2 R3 23 | 6 CD2 R3 24 | 7 CE2 R1 R3 25 | 8 H13 R1 26 | 9 H11 R1 27 | 10 H12 R1 28 | 11 HD1 R2 29 | 12 HD2 R3 30 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/tyr.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | TYR 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3001 23 | 24 | [ mapping ] 25 | amber27 amber36 26 | 27 | [ atoms ] 28 | 1 N BB 29 | 2 HN BB 30 | 3 CA BB 31 | 4 HA !BB 32 | 5 CB SC1 33 | 6 HB1 !SC1 34 | 7 HB2 !SC1 35 | 8 CG SC1 36 | 9 CD1 SC2 37 | 10 HD1 SC2 38 | 11 CE1 SC2 39 | 12 HE1 SC2 40 | 13 CZ SC4 41 | 14 OH SC4 42 | 15 HH SC4 43 | 16 CD2 SC3 44 | 17 HD2 SC3 45 | 18 CE2 SC3 46 | 19 HE2 SC3 47 | 20 C BB 48 | 21 O BB 49 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/tyr.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | TYR 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini3001 23 | 24 | [ mapping ] 25 | charmm27 charmm36 26 | 27 | [ atoms ] 28 | 1 N BB 29 | 2 HN BB 30 | 3 CA BB 31 | 4 HA !BB 32 | 5 CB SC1 33 | 6 HB1 !SC1 34 | 7 HB2 !SC1 35 | 8 CG SC1 36 | 9 CD1 SC2 37 | 10 HD1 SC2 38 | 11 CE1 SC2 39 | 12 HE1 SC2 40 | 13 CZ SC4 41 | 14 OH SC4 42 | 15 HH SC4 43 | 16 CD2 SC3 44 | 17 HD2 SC3 45 | 18 CE2 SC3 46 | 19 HE2 SC3 47 | 20 C BB 48 | 21 O BB 49 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/zimi.charmm36.map: -------------------------------------------------------------------------------- 1 | ; BZIM 2 | [ molecule ] 3 | ZIMI 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | N4 R1 N5 R2 R3 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C7 R2 19 | 2 C6 R1 20 | 3 C5 R1 21 | 4 C4 R3 22 | 5 C9 R3 23 | 6 C8 R2 24 | 7 N1 N5 25 | 8 H1 N5 26 | 9 C2 N4 N5 27 | 10 N3 N4 28 | 11 H7 R2 29 | 12 H6 R1 30 | 13 H5 R1 31 | 14 H8 R2 32 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/zthp.charmm36.map: -------------------------------------------------------------------------------- 1 | ; BZTH 2 | [ molecule ] 3 | ZTHP 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R1 R5 R2 S4 R3 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 C3 R5 19 | 2 C4 R3 20 | 3 C5 R2 21 | 4 C6 R2 22 | 5 C7 R1 23 | 6 C8 R1 24 | 7 C9 R3 25 | 8 S1 S4 26 | 9 C2 R5 27 | 10 H3 R5 28 | 11 H5 R2 29 | 12 H6 R2 30 | 13 H7 R1 31 | 14 H8 R1 32 | 15 H2 R5 33 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3001/zthz.charmm36.map: -------------------------------------------------------------------------------- 1 | ; BZTA 2 | [ molecule ] 3 | ZTHZ 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini3001 10 | 11 | [ martini ] 12 | R1 N5 R2 S4 R3 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 N3 N5 19 | 2 C4 R3 20 | 3 C5 R2 21 | 4 C6 R2 22 | 5 C7 R1 23 | 6 C8 R1 24 | 7 C9 R3 25 | 8 S1 S4 26 | 9 C2 N5 27 | 10 H5 R2 28 | 11 H6 R2 29 | 12 H7 R1 30 | 13 H8 R1 31 | 14 H2 N5 32 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini30b32/ala.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ALA 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini30b32 23 | 24 | [ martini ] 25 | BB 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB BB 36 | 6 HB1 !BB 37 | 7 HB2 !BB 38 | 8 HB3 !BB 39 | 9 C BB 40 | 10 O BB 41 | 42 | [ chiral ] 43 | CB CA N C 44 | HB1 CA N C 45 | HB2 CA N C 46 | HB3 CA N C 47 | 48 | [ chiral ] 49 | HA CA N CB C ; L-Ala 50 | ; HA CA N C CB ; D-Ala 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini30b32/asp.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ASP 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini30b32 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 CG SC1 39 | 9 OD1 SC1 40 | 10 OD2 SC1 41 | 11 HD2 !SC1 42 | 12 C BB 43 | 13 O BB 44 | 45 | [ chiral ] 46 | CB CA N C 47 | HB1 CA N C 48 | HB2 CA N C 49 | 50 | [ chiral ] 51 | HA CA N CB C ; L-Asp 52 | ; HA CA N C CB ; D-Asp 53 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini30b32/benz.charmm36.map: -------------------------------------------------------------------------------- 1 | ; BENZ 2 | [ molecule ] 3 | BENZ 4 | 5 | [ from ] 6 | charmm 7 | 8 | [ to ] 9 | martini30b32 10 | 11 | [ martini ] 12 | R2 R3 R1 13 | 14 | [ mapping ] 15 | charmm 16 | 17 | [ atoms ] 18 | 1 CG R3 19 | 2 CD1 R1 20 | 3 CE1 R1 21 | 4 CZ R2 22 | 5 CE2 R2 23 | 6 CD2 R3 24 | 7 HG R3 25 | 8 HD1 R1 26 | 9 HE1 R1 27 | 10 HZ R2 28 | 11 HE2 R2 29 | 12 HD2 R3 30 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini30b32/cys.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | CYS 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini30b32 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 SG SC1 39 | 9 HG1 !SC1 40 | 10 C BB 41 | 11 O BB 42 | 43 | [ chiral ] 44 | CB CA N C 45 | HB1 CA N C 46 | HB2 CA N C 47 | 48 | [ chiral ] 49 | HA CA N CB C ; L-Cys 50 | ; HA CA N C CB ; D-Cys 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini30b32/gly.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | GLY 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini30b32 23 | 24 | [ martini ] 25 | BB 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA1 !BB 35 | 5 HA2 !BB 36 | 9 C BB 37 | 10 O BB 38 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini30b32/modifications.mapping: -------------------------------------------------------------------------------- 1 | [ modification ] 2 | [ from ] 3 | charmm 4 | [ to ] 5 | martini30b32 6 | 7 | [ from blocks ] 8 | C-ter 9 | [ to blocks ] 10 | C-ter 11 | 12 | [ from nodes ] 13 | N 14 | HN 15 | 16 | [ from edges ] 17 | HN N 18 | N CA 19 | 20 | [ mapping ] 21 | CA BB 22 | C BB 23 | O BB 24 | OXT BB 25 | 26 | 27 | [modification] 28 | [ from ] 29 | charmm 30 | [ to ] 31 | martini30b32 32 | [ from blocks ] 33 | N-ter 34 | [ to blocks ] 35 | N-ter 36 | 37 | [ from nodes ] 38 | C 39 | O 40 | 41 | [ from edges ] 42 | C O 43 | CA C 44 | 45 | [ mapping ] 46 | HN2 BB 47 | HN3 BB 48 | N BB 49 | CA BB 50 | C BB 51 | O BB 52 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini30b32/ser.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | SER 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini30b32 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 OG SC1 39 | 9 HG1 SC1 40 | 10 C BB 41 | 11 O BB 42 | 43 | [ chiral ] 44 | CB CA N C 45 | HB1 CA N C 46 | HB2 CA N C 47 | 48 | [ chiral ] 49 | HA CA N CB C ; L-Ser 50 | ; HA CA N C CB ; D-Ser 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini30b32/tyr.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | TYR 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini30b32 23 | 24 | [ mapping ] 25 | charmm27 charmm36 26 | 27 | [ atoms ] 28 | 1 N BB 29 | 2 HN BB 30 | 3 CA BB 31 | 4 HA !BB 32 | 5 CB SC1 33 | 6 HB1 !SC1 34 | 7 HB2 !SC1 35 | 8 CG SC1 36 | 9 CD1 SC2 37 | 10 HD1 SC2 38 | 11 CE1 SC2 39 | 12 HE1 SC2 40 | 13 CZ SC4 41 | 14 OH SC4 42 | 15 HH SC4 43 | 16 CD2 SC3 44 | 17 HD2 SC3 45 | 18 CE2 SC3 46 | 19 HE2 SC3 47 | 20 C BB 48 | 21 O BB 49 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3IDP/ala.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ALA 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3IDP 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | amber27 amber36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 HB3 !SC1 39 | 9 C BB 40 | 10 O BB 41 | 42 | [ chiral ] 43 | CB CA N C 44 | HB1 CA N C 45 | HB2 CA N C 46 | HB3 CA N C 47 | 48 | [ chiral ] 49 | HA CA N CB C ; L-Ala 50 | ; HA CA N C CB ; D-Ala 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3IDP/ala.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ALA 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini3IDP 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 HB3 !SC1 39 | 9 C BB 40 | 10 O BB 41 | 42 | [ chiral ] 43 | CB CA N C 44 | HB1 CA N C 45 | HB2 CA N C 46 | HB3 CA N C 47 | 48 | [ chiral ] 49 | HA CA N CB C ; L-Ala 50 | ; HA CA N C CB ; D-Ala 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3IDP/asp.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ASP 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3IDP 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | amber27 amber36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 CG SC1 39 | 9 OD1 SC1 40 | 10 OD2 SC1 41 | 11 HD2 !SC1 42 | 12 C BB 43 | 13 O BB 44 | 45 | [ chiral ] 46 | CB CA N C 47 | HB1 CA N C 48 | HB2 CA N C 49 | 50 | [ chiral ] 51 | HA CA N CB C ; L-Asp 52 | ; HA CA N C CB ; D-Asp 53 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3IDP/asp.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ASP 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini3IDP 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 CG SC1 39 | 9 OD1 SC1 40 | 10 OD2 SC1 41 | 11 HD2 !SC1 42 | 12 C BB 43 | 13 O BB 44 | 45 | [ chiral ] 46 | CB CA N C 47 | HB1 CA N C 48 | HB2 CA N C 49 | 50 | [ chiral ] 51 | HA CA N CB C ; L-Asp 52 | ; HA CA N C CB ; D-Asp 53 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3IDP/aspp.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | ASPP 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini3IDP 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 CG SC1 39 | 9 OD1 SC1 40 | 10 OD2 SC1 41 | 11 HD2 !SC1 42 | 12 C BB 43 | 13 O BB 44 | 45 | [ chiral ] 46 | CB CA N C 47 | HB1 CA N C 48 | HB2 CA N C 49 | 50 | [ chiral ] 51 | HA CA N CB C ; L-Asp 52 | ; HA CA N C CB ; D-Asp 53 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3IDP/cys.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | CYS 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3IDP 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | amber27 amber36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 SG SC1 39 | 9 HG1 !SC1 40 | 10 C BB 41 | 11 O BB 42 | 43 | [ chiral ] 44 | CB CA N C 45 | HB1 CA N C 46 | HB2 CA N C 47 | 48 | [ chiral ] 49 | HA CA N CB C ; L-Cys 50 | ; HA CA N C CB ; D-Cys 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3IDP/cys.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | CYS 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini3IDP 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 SG SC1 39 | 9 HG1 !SC1 40 | 10 C BB 41 | 11 O BB 42 | 43 | [ chiral ] 44 | CB CA N C 45 | HB1 CA N C 46 | HB2 CA N C 47 | 48 | [ chiral ] 49 | HA CA N CB C ; L-Cys 50 | ; HA CA N C CB ; D-Cys 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3IDP/gly.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | GLY 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3IDP 23 | 24 | [ martini ] 25 | BB 26 | 27 | [ mapping ] 28 | amber27 amber36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA1 !BB 35 | 5 HA2 !BB 36 | 9 C BB 37 | 10 O BB 38 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3IDP/gly.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | GLY 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini3IDP 23 | 24 | [ martini ] 25 | BB 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA1 !BB 35 | 5 HA2 !BB 36 | 9 C BB 37 | 10 O BB 38 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3IDP/hid.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | HID 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3IDP 23 | 24 | [ martini ] 25 | BB SC1 SC2 SC3 26 | 27 | [ mapping ] 28 | amber 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 H BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 CG SC2 39 | 9 ND1 SC2 40 | 10 HD1 SC1 41 | 11 CE1 SC2 42 | 12 HE1 SC2 43 | 13 NE2 SC3 44 | 14 CD2 SC3 45 | 15 HD2 SC3 46 | 16 C BB 47 | 17 O BB 48 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3IDP/his.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | HIS 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3IDP 23 | 24 | [ martini ] 25 | BB SC1 SC2 SC3 26 | 27 | [ mapping ] 28 | amber27 amber36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 CD2 SC2 39 | 9 HD2 SC2 40 | 10 CG SC1 41 | 11 NE2 SC2 42 | 12 HE2 SC2 43 | 13 ND1 SC3 44 | 14 CE1 SC3 45 | 15 C BB 46 | 16 O BB 47 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3IDP/ser.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | SER 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3IDP 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | amber27 amber36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 OG SC1 39 | 9 HG1 SC1 40 | 10 C BB 41 | 11 O BB 42 | 43 | [ chiral ] 44 | CB CA N C 45 | HB1 CA N C 46 | HB2 CA N C 47 | 48 | [ chiral ] 49 | HA CA N CB C ; L-Ser 50 | ; HA CA N C CB ; D-Ser 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3IDP/ser.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | SER 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini3IDP 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 4 HA !BB 35 | 5 CB SC1 36 | 6 HB1 !SC1 37 | 7 HB2 !SC1 38 | 8 OG SC1 39 | 9 HG1 SC1 40 | 10 C BB 41 | 11 O BB 42 | 43 | [ chiral ] 44 | CB CA N C 45 | HB1 CA N C 46 | HB2 CA N C 47 | 48 | [ chiral ] 49 | HA CA N CB C ; L-Ser 50 | ; HA CA N C CB ; D-Ser 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3IDP/tyr.amber.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | TYR 17 | 18 | [from] 19 | amber 20 | 21 | [to] 22 | martini3IDP 23 | 24 | [ mapping ] 25 | amber27 amber36 26 | 27 | [ atoms ] 28 | 1 N BB 29 | 2 HN BB 30 | 3 CA BB 31 | 4 HA !BB 32 | 5 CB SC1 33 | 6 HB1 !SC1 34 | 7 HB2 !SC1 35 | 8 CG SC1 36 | 9 CD1 SC2 37 | 10 HD1 SC2 38 | 11 CE1 SC2 39 | 12 HE1 SC2 40 | 13 CZ SC4 41 | 14 OH SC4 42 | 15 HH SC4 43 | 16 CD2 SC3 44 | 17 HD2 SC3 45 | 18 CE2 SC3 46 | 19 HE2 SC3 47 | 20 C BB 48 | 21 O BB 49 | -------------------------------------------------------------------------------- /vermouth/data/mappings/martini3IDP/tyr.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | TYR 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini3IDP 23 | 24 | [ mapping ] 25 | charmm27 charmm36 26 | 27 | [ atoms ] 28 | 1 N BB 29 | 2 HN BB 30 | 3 CA BB 31 | 4 HA !BB 32 | 5 CB SC1 33 | 6 HB1 !SC1 34 | 7 HB2 !SC1 35 | 8 CG SC1 36 | 9 CD1 SC2 37 | 10 HD1 SC2 38 | 11 CE1 SC2 39 | 12 HE1 SC2 40 | 13 CZ SC4 41 | 14 OH SC4 42 | 15 HH SC4 43 | 16 CD2 SC3 44 | 17 HD2 SC3 45 | 18 CE2 SC3 46 | 19 HE2 SC3 47 | 20 C BB 48 | 21 O BB 49 | -------------------------------------------------------------------------------- /vermouth/data/mappings/met.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | MET 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB SC1 BB BB 21 | 5 CG SC1 BB 22 | 6 SD SC1 SC1 BB 23 | 7 CE SC1 24 | 8 C BB 25 | 9 O BB 26 | 27 | -------------------------------------------------------------------------------- /vermouth/data/mappings/modifications.gromos.mapping: -------------------------------------------------------------------------------- 1 | [ modification ] 2 | [ from ] 3 | gromos 4 | [ to ] 5 | martini22 6 | 7 | [ from blocks ] 8 | C-ter 9 | [ to blocks ] 10 | C-ter 11 | 12 | [ from nodes ] 13 | N 14 | HN 15 | 16 | [ from edges ] 17 | HN N 18 | N CA 19 | 20 | [ mapping ] 21 | CA BB 22 | C BB 23 | O BB 24 | OXT BB 25 | 26 | 27 | [modification] 28 | [ from ] 29 | gromos 30 | [ to ] 31 | martini22 32 | [ from blocks ] 33 | N-ter 34 | [ to blocks ] 35 | N-ter 36 | 37 | [ from nodes ] 38 | C 39 | O 40 | 41 | [ from edges ] 42 | C O 43 | CA C 44 | 45 | [ mapping ] 46 | HN2 BB 47 | HN3 BB 48 | N BB 49 | CA BB 50 | C BB 51 | O BB 52 | -------------------------------------------------------------------------------- /vermouth/data/mappings/phe.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | PHE 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 SC2 SC3 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB SC1 BB 21 | 5 CG SC1 22 | 6 CD1 SC1 SC3 23 | 7 HD1 SC1 24 | 8 CD2 SC2 SC1 25 | 9 HD2 SC2 26 | ; 10 CE1 SC3 SC3 SC3 SC1 SC2 27 | 10 CE1 SC3 28 | 11 HE1 SC3 29 | ; 12 CE2 SC2 SC2 SC2 SC1 SC3 30 | 12 CE2 SC2 31 | 13 HE2 SC2 32 | 14 CZ SC3 SC2 33 | 15 HZ SC3 34 | 16 C BB 35 | 17 O BB 36 | 37 | -------------------------------------------------------------------------------- /vermouth/data/mappings/pro.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | PRO 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini22 23 | martini22p 24 | 25 | [ martini ] 26 | BB SC1 27 | 28 | [ mapping ] 29 | charmm27 charmm36 30 | 31 | [ atoms ] 32 | 1 N BB 33 | 2 CD SC1 34 | 3 CA BB 35 | 4 CB SC1 36 | 5 CG SC1 37 | 6 C BB 38 | 7 O BB 39 | 40 | [ chiral ] 41 | CB CA N C 42 | HB1 CA N C 43 | HB2 CA N C 44 | 45 | [ chiral ] 46 | HA CA N CB C ; L-Pro 47 | ; HA CA N C CB ; D-Pro 48 | -------------------------------------------------------------------------------- /vermouth/data/mappings/pro.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | PRO 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 CA BB 19 | 3 CB SC1 BB 20 | 4 CG SC1 21 | 5 CD SC1 22 | 6 C BB 23 | 7 O BB 24 | 25 | -------------------------------------------------------------------------------- /vermouth/data/mappings/ser.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | SER 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini22 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 5 CB SC1 35 | 8 OG SC1 36 | 9 HG1 SC1 37 | 10 C BB 38 | 11 O BB 39 | 40 | [ chiral ] 41 | CB CA N C 42 | HB1 CA N C 43 | HB2 CA N C 44 | 45 | [ chiral ] 46 | HA CA N CB C ; L-Ser 47 | ; HA CA N C CB ; D-Ser 48 | -------------------------------------------------------------------------------- /vermouth/data/mappings/ser.charmm36.martini22p.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | SER 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini22p 23 | 24 | [ martini ] 25 | BB SC1 26 | 27 | [ mapping ] 28 | charmm27 charmm36 29 | 30 | [ atoms ] 31 | 1 N BB 32 | 2 HN BB 33 | 3 CA BB 34 | 5 CB SC1 35 | 8 OG SC1 36 | 9 HG1 SC1 37 | 10 C BB 38 | 11 O BB 39 | 40 | [ chiral ] 41 | CB CA N C 42 | HB1 CA N C 43 | HB2 CA N C 44 | 45 | [ chiral ] 46 | HA CA N CB C ; L-Ser 47 | ; HA CA N C CB ; D-Ser 48 | 49 | [ extra ] 50 | SCP SCN 51 | -------------------------------------------------------------------------------- /vermouth/data/mappings/ser.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | SER 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB SC1 BB BB 21 | 5 OG SC1 SC1 BB 22 | 6 HG SC1 23 | 7 C BB 24 | 8 O BB 25 | 26 | -------------------------------------------------------------------------------- /vermouth/data/mappings/thr.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | THR 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB SC1 BB BB 21 | 5 OG1 SC1 SC1 BB 22 | 6 HG1 SC1 23 | 7 CG2 SC1 SC1 BB 24 | 8 C BB 25 | 9 O BB 26 | 27 | -------------------------------------------------------------------------------- /vermouth/data/mappings/tpp.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | TPP 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | THI1 THI2 THI3 THI4 THI5 PO4A PO4B 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N1 THI1 18 | 2 H1 THI1 19 | 3 H2 THI1 20 | 4 C1 THI1 21 | 5 N2 THI1 22 | 6 C2 THI2 23 | 7 C3 THI2 24 | 8 N3 THI2 25 | 9 C4 THI3 26 | 10 H3 THI3 27 | 11 C5 THI3 28 | 12 C6 THI3 29 | 13 N4 THI4 30 | 14 C7 THI4 31 | 15 C8 THI4 32 | 16 C9 THI5 33 | 17 S1 THI5 34 | 18 C10 THI4 35 | 19 H4 THI4 36 | 20 C11 THI5 37 | 21 C12 THI5 38 | 22 O1PA THI5 PO4A 39 | 23 PA PO4A 40 | 24 O2PA PO4A 41 | 25 O3PA PO4A 42 | 26 O1PG PO4A PO4B 43 | 27 PG PO4B 44 | 28 O2PG PO4B 45 | 29 O3PG PO4B 46 | 30 O4PG PO4B 47 | -------------------------------------------------------------------------------- /vermouth/data/mappings/trp.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | TRP 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 SC2 SC3 SC4 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB SC1 BB 21 | 5 CG SC1 SC1 SC1 SC1 SC3 SC3 22 | 6 CD1 SC1 23 | 7 HD1 SC1 24 | 8 CD2 SC3 SC3 SC2 25 | 9 NE1 SC2 SC1 26 | 10 HE1 SC2 27 | 11 CE2 SC2 SC2 SC3 28 | 12 CE3 SC3 SC3 SC4 29 | 13 HE3 SC3 30 | 14 CZ2 SC2 SC2 SC4 31 | 15 HZ2 SC2 32 | 16 CZ3 SC4 SC4 SC3 33 | 17 HZ3 SC4 34 | 18 CH2 SC4 SC4 SC2 35 | 19 HH2 SC4 36 | 20 C BB 37 | 21 O BB 38 | 39 | [ trans ] 40 | CB CG CD2 CE2 41 | HD1 CD1 NE1 CE2 42 | HE1 NE1 CD1 CG 43 | HE3 CE3 CD2 CE2 44 | HZ2 CZ2 CE2 CD2 45 | HZ3 CZ3 CE3 CD2 46 | HH2 CH2 CZ3 CE3 47 | 48 | [ chiral ] 49 | CB CA N C 50 | 51 | 52 | 53 | -------------------------------------------------------------------------------- /vermouth/data/mappings/tyr.gromos.map: -------------------------------------------------------------------------------- 1 | ;22.01.13 fixed by kri positions of OH and HH 2 | [ molecule ] 3 | TYR 4 | 5 | [from] 6 | gromos 7 | 8 | [to] 9 | martini22 10 | 11 | [ martini ] 12 | BB SC1 SC2 SC3 13 | 14 | [ mapping ] 15 | gromos 16 | 17 | [ atoms ] 18 | 1 N BB 19 | 2 H BB 20 | 3 CA BB 21 | 4 CB SC1 BB 22 | 5 CG SC1 23 | 6 CD1 SC1 SC3 24 | 7 HD1 SC1 25 | 8 CD2 SC2 SC1 26 | 9 HD2 SC2 27 | ; 10 CE1 SC3 SC3 SC3 SC1 SC2 28 | 10 CE1 SC3 29 | 11 HE1 SC3 30 | ; 12 CE2 SC2 SC2 SC2 SC1 SC3 31 | 12 CE2 SC2 32 | 13 HE2 SC2 33 | 14 CZ SC3 SC3 SC1 SC2 SC2 34 | 15 OH SC3 SC3 SC2 35 | 16 HH SC3 36 | 17 C BB 37 | 18 O BB 38 | 39 | 40 | -------------------------------------------------------------------------------- /vermouth/data/mappings/val.charmm36.map: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ molecule ] 16 | VAL 17 | 18 | [from] 19 | charmm 20 | 21 | [to] 22 | martini22 23 | martini22p 24 | 25 | [ martini ] 26 | BB SC1 27 | 28 | [ mapping ] 29 | charmm27 charmm36 30 | 31 | [ atoms ] 32 | 1 N BB 33 | 2 HN BB 34 | 3 CA BB 35 | 5 CB SC1 36 | 8 CG1 SC1 37 | 12 CG2 SC1 38 | 16 C BB 39 | 17 O BB 40 | 41 | [ chiral ] 42 | CB CA N C 43 | HB CA N C 44 | 45 | [ chiral ] 46 | HA CA N CB C ; L-Val 47 | ; HA CA N C CB ; D-Val 48 | 49 | [ out ] 50 | CG2 CB CG1 CA 51 | HG21 CB CG1 CA 52 | HG22 CB CG1 CA 53 | HG23 CB CG1 CA 54 | -------------------------------------------------------------------------------- /vermouth/data/mappings/val.gromos.map: -------------------------------------------------------------------------------- 1 | [ molecule ] 2 | VAL 3 | 4 | [from] 5 | gromos 6 | 7 | [to] 8 | martini22 9 | 10 | [ martini ] 11 | BB SC1 12 | 13 | [ mapping ] 14 | gromos 15 | 16 | [ atoms ] 17 | 1 N BB 18 | 2 H BB 19 | 3 CA BB 20 | 4 CB SC1 BB 21 | 5 CG1 SC1 22 | 6 CG2 SC1 23 | 7 C BB 24 | 8 O BB 25 | 26 | -------------------------------------------------------------------------------- /vermouth/dssp/__init__.py: -------------------------------------------------------------------------------- 1 | # Copyright 2018 University of Groningen 2 | # 3 | # Licensed under the Apache License, Version 2.0 (the "License"); 4 | # you may not use this file except in compliance with the License. 5 | # You may obtain a copy of the License at 6 | # 7 | # http://www.apache.org/licenses/LICENSE-2.0 8 | # 9 | # Unless required by applicable law or agreed to in writing, software 10 | # distributed under the License is distributed on an "AS IS" BASIS, 11 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | # See the License for the specific language governing permissions and 13 | # limitations under the License. 14 | -------------------------------------------------------------------------------- /vermouth/gmx/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # Copyright 2018 University of Groningen 3 | # 4 | # Licensed under the Apache License, Version 2.0 (the "License"); 5 | # you may not use this file except in compliance with the License. 6 | # You may obtain a copy of the License at 7 | # 8 | # http://www.apache.org/licenses/LICENSE-2.0 9 | # 10 | # Unless required by applicable law or agreed to in writing, software 11 | # distributed under the License is distributed on an "AS IS" BASIS, 12 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | # See the License for the specific language governing permissions and 14 | # limitations under the License. 15 | """ 16 | Provides functionality to read and write Gromacs specific files. 17 | """ 18 | 19 | 20 | from .gro import read_gro, write_gro 21 | from .itp import write_molecule_itp 22 | from .itp_read import read_itp 23 | from .rtp import read_rtp 24 | -------------------------------------------------------------------------------- /vermouth/pdb/__init__.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # Copyright 2018 University of Groningen 3 | # 4 | # Licensed under the Apache License, Version 2.0 (the "License"); 5 | # you may not use this file except in compliance with the License. 6 | # You may obtain a copy of the License at 7 | # 8 | # http://www.apache.org/licenses/LICENSE-2.0 9 | # 10 | # Unless required by applicable law or agreed to in writing, software 11 | # distributed under the License is distributed on an "AS IS" BASIS, 12 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | # See the License for the specific language governing permissions and 14 | # limitations under the License. 15 | """ 16 | Provides functionality to read and write PDB files. 17 | """ 18 | 19 | from .pdb import read_pdb, write_pdb 20 | from .cif import CIFReader 21 | -------------------------------------------------------------------------------- /vermouth/processors/set_molecule_meta.py: -------------------------------------------------------------------------------- 1 | # Copyright 2018 University of Groningen 2 | # 3 | # Licensed under the Apache License, Version 2.0 (the "License"); 4 | # you may not use this file except in compliance with the License. 5 | # You may obtain a copy of the License at 6 | # 7 | # http://www.apache.org/licenses/LICENSE-2.0 8 | # 9 | # Unless required by applicable law or agreed to in writing, software 10 | # distributed under the License is distributed on an "AS IS" BASIS, 11 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | # See the License for the specific language governing permissions and 13 | # limitations under the License. 14 | 15 | from .processor import Processor 16 | 17 | 18 | class SetMoleculeMeta(Processor): 19 | def __init__(self, **meta): 20 | self.meta = meta 21 | super().__init__() 22 | 23 | def run_molecule(self, molecule): 24 | molecule.meta.update(self.meta) 25 | return molecule 26 | -------------------------------------------------------------------------------- /vermouth/rcsu/__init__.py: -------------------------------------------------------------------------------- 1 | 2 | -------------------------------------------------------------------------------- /vermouth/tests/__init__.py: -------------------------------------------------------------------------------- 1 | # Copyright 2018 University of Groningen 2 | # 3 | # Licensed under the Apache License, Version 2.0 (the "License"); 4 | # you may not use this file except in compliance with the License. 5 | # You may obtain a copy of the License at 6 | # 7 | # http://www.apache.org/licenses/LICENSE-2.0 8 | # 9 | # Unless required by applicable law or agreed to in writing, software 10 | # distributed under the License is distributed on an "AS IS" BASIS, 11 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | # See the License for the specific language governing permissions and 13 | # limitations under the License. 14 | -------------------------------------------------------------------------------- /vermouth/tests/data/ala5_cg.pdb: -------------------------------------------------------------------------------- 1 | ATOM 1 CA ALA A 1 0.673 0.000 0.000 1.00 0.00 2 | ATOM 2 BB ALA A 1 2.161 1.828 0.000 1.00 0.00 3 | ATOM 3 CA ALA A 2 3.988 2.839 0.000 1.00 0.00 4 | ATOM 4 BB ALA A 2 5.937 2.646 0.000 1.00 0.00 5 | ATOM 5 CA ALA A 3 7.660 3.823 0.000 1.00 0.00 6 | ATOM 6 BB ALA A 3 8.363 5.651 0.000 1.00 0.00 7 | ATOM 7 CA ALA A 4 10.190 6.661 0.000 1.00 0.00 8 | ATOM 8 BB ALA A 4 12.139 6.468 0.000 1.00 0.00 9 | ATOM 9 CA ALA A 5 13.862 7.646 0.000 1.00 0.00 10 | ATOM 10 BB ALA A 5 14.571 9.473 0.000 1.00 0.00 11 | TER 11 ALA A 5 12 | CONECT 1 2 13 | CONECT 2 3 14 | CONECT 3 4 15 | CONECT 4 5 16 | CONECT 5 6 17 | CONECT 6 7 18 | CONECT 7 8 19 | CONECT 8 9 20 | CONECT 9 10 21 | END -------------------------------------------------------------------------------- /vermouth/tests/data/force_fields/pepplane/ala.ff: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ macros ] 16 | protein_resnames "GLY|ALA|CYS|VAL|LEU|ILE|MET|PRO|HYP|ASN|GLN|ASP|ASP0|GLU|GLU0|THR|SER|LYS|LYS0|ARG|ARG0|HIS|HISH|PHE|TYR|TRP" 17 | protein_resnames_non_pro "GLY|ALA|CYS|VAL|LEU|ILE|MET|ASN|GLN|ASP|ASP0|GLU|GLU0|THR|SER|LYS|LYS0|ARG|ARG0|HIS|HISH|PHE|TYR|TRP" 18 | 19 | ;;; ALANINE 20 | 21 | [ moleculetype ] 22 | ; molname nrexcl 23 | ALA 1 24 | 25 | [ atoms ] 26 | ;id type resnr residu atom cgnr charge 27 | 1 P4 1 ALA BB 1 0 ; ALA slightly less polar 28 | 2 D 1 ALA CA 2 0 29 | 30 | [bonds] 31 | 1 2 1 0.31 7500 32 | 33 | -------------------------------------------------------------------------------- /vermouth/tests/data/force_fields/pepplane/general.ff: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ variables ] 16 | center_weight "mass" 17 | -------------------------------------------------------------------------------- /vermouth/tests/data/force_fields/pepplane/modifications.ff: -------------------------------------------------------------------------------- 1 | [ modification ] 2 | C-ter 3 | [ atoms ] 4 | BB {"PTM_atom": true, "atype": "Qa", "charge": -1} 5 | 6 | [ modification ] 7 | N-ter 8 | [ atoms ] 9 | CA {"PTM_atom": true, "atype": "Qd", "charge": 1} 10 | 11 | [ modification ] 12 | zwitter 13 | [ atoms ] 14 | BB {"replace": {"atype": "Qda", "charge": 0}} 15 | 16 | 17 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/dipro-termini/README: -------------------------------------------------------------------------------- 1 | # Test with a PRO-PRO dipeptide to make sure neutral termini can be applied to proline -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/cg.pdb: -------------------------------------------------------------------------------- 1 | ATOM 1 BB PRO 1 0.674 1.038 0.858 1.00 0.00 2 | ATOM 2 SC1 PRO 1 -0.474 -0.386 -0.292 1.00 0.00 3 | ATOM 3 BB PRO 2 1.271 4.576 0.417 1.00 0.00 4 | ATOM 4 SC1 PRO 2 3.612 3.464 0.289 1.00 0.00 5 | TER 5 PRO 2 6 | CONECT 1 2 3 7 | CONECT 3 4 8 | END -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/citation: -------------------------------------------------------------------------------- 1 | Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -x cg.pdb 4 | -o topol.top 5 | -ff martini3001 6 | -nt 7 | -noscfix 8 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/molecule_0.itp: -------------------------------------------------------------------------------- 1 | ; This file was generated using the following command: 2 | ; /homes/peterkroon/virtualenvs/martinize2/bin/martinize2 -f ../aa.pdb -x cg.pdb -o topol.top -ff martini3001 -nt 3 | ; martinize with vermouth 0.7.4.dev121 4 | 5 | ; Pleas cite the following papers: 6 | ; Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 7 | 8 | [ moleculetype ] 9 | molecule_0 1 10 | 11 | [ atoms ] 12 | 1 P6 1 PRO BB 1 0 13 | 2 SC3 1 PRO SC1 2 0.0 14 | 3 P6 2 PRO BB 3 0 15 | 4 SC3 2 PRO SC1 4 0.0 16 | 17 | [ bonds ] 18 | ; Backbone bonds 19 | 1 3 1 0.350 4000 20 | 21 | ; Side chain bonds 22 | 1 2 1 0.330 7500 23 | 3 4 1 0.330 7500 24 | 25 | [ angles ] 26 | ; BBS angles regular martini 27 | 1 3 4 2 100 25 28 | 29 | ; First SBB regular martini 30 | 2 1 3 2 100 25 31 | 32 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/dipro-termini/martinize2/topol.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # Original PDB CODE: 1ICO 4 | # Structure from NMR experiment: select the first model to martinize 5 | # Replace the residue name DPR (d-proline, residue 8) and DAL (d-alanine, residue 23) for PRO and ALA 6 | # Maybe could be used to test d- amino acids 7 | 8 | ### TEST: 9 | 10 | # -ff martini22 11 | # -cys auto 12 | # -dssp 13 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/citation: -------------------------------------------------------------------------------- 1 | Marrink, S J; Risselada, H J; Yefimov, S; Tieleman, D P; De Vries, A H; The journal of physical chemistry B 2007 2 | de Jong, D H; Singh, G; Bennett, W D; Arnarez, C; Wassenaar, T A; Schaefer, L V; Periole, X; Tieleman, D P; Marrink, S J; Journal of chemical theory and computation 2013 3 | Monticelli, L; Kandasamy, S K; Periole, X; Larson, R G; Tieleman, D P; Marrink, S J; Journal of chemical theory and computation 2008 4 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -x cg.pdb 4 | -o topol.top 5 | -ff martini22 6 | -dssp 7 | -cys auto 8 | -noscfix 9 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/screen.output: -------------------------------------------------------------------------------- 1 | INFO - general - Read 1 molecules from PDB file ../aa.pdb 2 | INFO - step - Guessing the bonds. 3 | INFO - general - 1 molecules after guessing bonds 4 | INFO - step - Repairing the graph. 5 | INFO - step - Dealing with modifications. 6 | INFO - general - Identified the modifications ['N-ter'] on residues ['SER1'] 7 | INFO - general - Identified the modifications ['C-ter'] on residues ['GLU29'] 8 | INFO - step - Read input. 9 | INFO - step - Creating the graph at the target resolution. 10 | INFO - general - Applying modification mapping ('N-ter',) 11 | INFO - general - Applying modification mapping ('C-ter',) 12 | INFO - step - Averaging the coordinates. 13 | INFO - step - Applying the links. 14 | INFO - step - Placing the charge dummies. 15 | INFO - step - Writing output. 16 | INFO - general - If you drink, don’t drive. Don’t even putt. -- Dean Martin 17 | 18 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein1_betasheet/martinize2/topol.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # Original PDB CODE:5UOI 4 | # Structure from NMR experiment: select the first model to martinize 5 | # One of the missing oxygen atoms of the C-terminal was added to make martinize2 to work. 6 | 7 | ### TEST: 8 | 9 | # -ff elnedyn 10 | # -ss 11 | # neutral terminis 12 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/citation: -------------------------------------------------------------------------------- 1 | Marrink, S J; Risselada, H J; Yefimov, S; Tieleman, D P; De Vries, A H; The journal of physical chemistry B 2007 2 | Monticelli, L; Kandasamy, S K; Periole, X; Larson, R G; Tieleman, D P; Marrink, S J; Journal of chemical theory and computation 2008 3 | Periole, X; Cavalli, M; Marrink, S J; Ceruso, M A; Journal of chemical theory and computation 2009 4 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -x cg.pdb 4 | -o topol.top 5 | -ff elnedyn21 6 | -ss CCSHHHHHHHHHHCCCCHHHHHHHHHHHTSCHHHHHHHTCCCC 7 | -nter NH2-ter 8 | -cter COOH-ter 9 | -ef 500 10 | -noscfix 11 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein2_helix/martinize2/topol.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # Original PDB CODE:1L2Y 4 | # Structure from NMR experiment: select the first model to martinize 5 | 6 | ### TEST: 7 | 8 | # -ff elnedyn22 9 | # -dssp 10 | # -eu 0.7 -ef 800.0 11 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/citation: -------------------------------------------------------------------------------- 1 | Marrink, S J; Risselada, H J; Yefimov, S; Tieleman, D P; De Vries, A H; The journal of physical chemistry B 2007 2 | de Jong, D H; Singh, G; Bennett, W D; Arnarez, C; Wassenaar, T A; Schaefer, L V; Periole, X; Tieleman, D P; Marrink, S J; Journal of chemical theory and computation 2013 3 | Monticelli, L; Kandasamy, S K; Periole, X; Larson, R G; Tieleman, D P; Marrink, S J; Journal of chemical theory and computation 2008 4 | Periole, X; Cavalli, M; Marrink, S J; Ceruso, M A; Journal of chemical theory and computation 2009 5 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -x cg.pdb 4 | -o topol.top 5 | -ff elnedyn22 6 | -dssp 7 | -eu 0.7 8 | -ef 800.0 9 | -noscfix 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/screen.output: -------------------------------------------------------------------------------- 1 | INFO - general - Read 1 molecules from PDB file ../aa.pdb 2 | INFO - step - Guessing the bonds. 3 | INFO - general - 1 molecules after guessing bonds 4 | INFO - step - Repairing the graph. 5 | INFO - step - Dealing with modifications. 6 | INFO - general - Identified the modifications ['N-ter'] on residues ['ASN1'] 7 | INFO - general - Identified the modifications ['C-ter'] on residues ['SER20'] 8 | INFO - step - Read input. 9 | INFO - step - Creating the graph at the target resolution. 10 | WARNING - general - Can't find modification mappings for the modifications ['C-ter']. The following modification mappings are known: {} 11 | WARNING - general - Can't find modification mappings for the modifications ['N-ter']. The following modification mappings are known: {} 12 | WARNING - unmapped-atom - These atoms are not covered by a mapping. Either your mappings don't describe all atoms (bad idea), or, there's no mapping available for all residues. ['299A-SER20:OXT'] 13 | INFO - step - Averaging the coordinates. 14 | INFO - step - Applying the links. 15 | INFO - step - Placing the charge dummies. 16 | INFO - step - Writing output. 17 | INFO - general - Happiness is a dry martini and a good woman... or a bad woman. -- George Burns 18 | 19 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-0/mini-protein3_trp-cage/martinize2/topol.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1UBQ/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # Ubiquitin 1UBQ 4 | 5 | ### testing 'new' defaults after -scfix and -ef behaviour changed 6 | 7 | ### TEST: 8 | 9 | # -ff martini 3001 10 | # no -scfix 11 | # 12 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/citation: -------------------------------------------------------------------------------- 1 | McGibbon, R T; Beauchamp, K A; Harrigan, M P; Klein, C; Swails, J M; Hernández, C X; Schwantes, C R; Wang, L; Lane, T J; Pande, V S; Biophysical Journal 2015; 10.1016/j.bpj.2015.08.015 2 | Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 3 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -ff martini3001 4 | -x cg.pdb 5 | -o topol.top 6 | -ignore HOH 7 | -dssp 8 | -elastic -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1UBQ/martinize2/topol.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/README: -------------------------------------------------------------------------------- 1 | Amber based pbd of 1mj5 2 | This test makes sure the protonation states 3 | of Histidine (i.e. HIE, HID, HIP) are correctly 4 | recognized 5 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/cg.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/citation: -------------------------------------------------------------------------------- 1 | Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 2 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5-charmm/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -o cg.top 4 | -x cg.pdb 5 | -ff martini3001 6 | -maxwarn 1 7 | -dssp 8 | -elastic 9 | -cys auto 10 | -ef 500 11 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5/README: -------------------------------------------------------------------------------- 1 | Amber based pbd of 1mj5 2 | This test makes sure the protonation states 3 | of Histidine (i.e. HIE, HID, HIP) are correctly 4 | recognized 5 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/cg.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/citation: -------------------------------------------------------------------------------- 1 | Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 2 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/1mj5/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -x cg.pdb 4 | -o cg.top 5 | -ff martini3001 6 | -elastic 7 | -cys auto 8 | -dssp 9 | -from amber 10 | -resid input 11 | -ef 500 12 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/3i40/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # The structure contains a homo-dimers where 4 | # the monomers are connected by 3 disulphide brdiges 5 | # one of the disulphide bridges has the same name 6 | # and resid in the dimers 7 | 8 | ### TEST: 9 | 10 | # - symmetric dishulphide bridge present 11 | # - merge but with new resids -> i.e. continious 12 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/cg.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/citation: -------------------------------------------------------------------------------- 1 | Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 2 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/3i40/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../3i40.pdb 3 | -o cg.top 4 | -x cg.pdb 5 | -dssp 6 | -p backbone 7 | -ff martini3001 8 | -cys auto 9 | -ignore HOH 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/6LFO_gap/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # The structure is based of 6LFO but with missing 4 | # loops. This generates 6 molecules on martinize2 5 | # level. In a merged molecule there should however 6 | # be gaps in the resid when the original ones are 7 | # kept. The last three resids are set to 900 to 8 | # check if some crazy value works 9 | 10 | ### TEST: 11 | 12 | # - keep old resids with gaps upon merge 13 | # - apply EN within all molecules 14 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/cg.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/citation: -------------------------------------------------------------------------------- 1 | Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 2 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/6LFO_gap/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../6LFO_gap.pdb 3 | -o cg.top 4 | -x cg.pdb 5 | -dssp 6 | -p backbone 7 | -ff martini3001 8 | -cys auto 9 | -ignore HOH 10 | -elastic 11 | -eunit all 12 | -resid input 13 | -ef 500 14 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_chain/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # Human Insulin HOMRO dimer 4 | # 2 chains which are connected by disulphide bridge 5 | 6 | ### TEST: 7 | 8 | # the test checks -eunit flag 9 | # with setting chain; no EN 10 | # bond should be formed between 11 | # the two chains 12 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/cg.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/citation: -------------------------------------------------------------------------------- 1 | Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 2 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_chain/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -o cg.top 4 | -x cg.pdb 5 | -dssp 6 | -p backbone 7 | -ff martini3001 8 | -cys auto 9 | -ignore HOH 10 | -elastic 11 | -eunit chain 12 | -ef 500 13 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_region/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # Human Insulin HOMRO dimer 4 | # 2 chains which are connected by disulphide bridge 5 | 6 | ### TEST: 7 | 8 | # the test checks -eunit flag 9 | # with setting region and a 10 | # residue range 11 | # elastic bonds should be formed 12 | # only within the regions within 13 | # the chains -> old_resids are used 14 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/cg.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/citation: -------------------------------------------------------------------------------- 1 | Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 2 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/EN_region/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -o cg.top 4 | -x cg.pdb 5 | -dssp 6 | -p backbone 7 | -ff martini3001 8 | -cys auto 9 | -ignore HOH 10 | -elastic 11 | -eunit 8:18 12 | -ef 500 13 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/bpti/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # Original PDB CODE: 4PTI 4 | # Structure from X-ray crystallography experiment. 5 | 6 | ### TEST: 7 | 8 | # -ff elnedy22 9 | # -force constant dependent of the distance 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/citation: -------------------------------------------------------------------------------- 1 | Marrink, S J; Risselada, H J; Yefimov, S; Tieleman, D P; De Vries, A H; The journal of physical chemistry B 2007 2 | de Jong, D H; Singh, G; Bennett, W D; Arnarez, C; Wassenaar, T A; Schaefer, L V; Periole, X; Tieleman, D P; Marrink, S J; Journal of chemical theory and computation 2013 3 | Monticelli, L; Kandasamy, S K; Periole, X; Larson, R G; Tieleman, D P; Marrink, S J; Journal of chemical theory and computation 2008 4 | Periole, X; Cavalli, M; Marrink, S J; Ceruso, M A; Journal of chemical theory and computation 2009 5 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -x cg.pdb 4 | -o topol.top 5 | -ff elnedyn22 6 | -dssp 7 | -cys auto 8 | -ea 0.8 9 | -ep 2 10 | -modify A-ASP50:ASP-HD2 11 | -ignore HOH 12 | -noscfix 13 | -ef 500 14 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/bpti/martinize2/topol.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/hst5/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # Histidin 5 peptide, IDP 4 | 5 | ### TEST: 6 | 7 | # -ff martini 3001 8 | # BB-W bias for idr 9 | # add extra IDR potentials 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/citation: -------------------------------------------------------------------------------- 1 | Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 2 | Souza, P C T; Araujo, L P B; Brasnett, C; Moreira, R A; Grunewald, F; Park, P; Wang, L; Razmazma, H; Borges-Araujo, A C; Cofas-Vargas, L F; Monticelli, L; Mera-Adasme, R; Melo, M N; Wu, S; Marrink, S J; Poma, A B; Thallmair, S; Nature Communications 2025; 10.1038/s41467-025-58719-0 3 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -ff martini3001 4 | -x cg.pdb 5 | -o topol.top 6 | -ss C 7 | -water-bias 8 | -water-bias-eps idr:0.5 9 | -id-regions 1:24 10 | -idr-tune 11 | -noscfix 12 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/topol.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | 4 | #include "virtual_sites_atomtypes.itp" 5 | #include "virtual_sites_nonbond_params.itp" 6 | #include "molecule_0.itp" 7 | 8 | [ system ] 9 | Title of the system 10 | 11 | [ molecules ] 12 | molecule_0 1 13 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/hst5/martinize2/virtual_sites_atomtypes.itp: -------------------------------------------------------------------------------- 1 | [ atomtypes ] 2 | molecule_0_1 0.0 0 A 0.00000000 0.00000000 3 | molecule_0_2 0.0 0 A 0.00000000 0.00000000 4 | molecule_0_3 0.0 0 A 0.00000000 0.00000000 5 | molecule_0_4 0.0 0 A 0.00000000 0.00000000 6 | molecule_0_5 0.0 0 A 0.00000000 0.00000000 7 | molecule_0_6 0.0 0 A 0.00000000 0.00000000 8 | molecule_0_7 0.0 0 A 0.00000000 0.00000000 9 | molecule_0_8 0.0 0 A 0.00000000 0.00000000 10 | molecule_0_9 0.0 0 A 0.00000000 0.00000000 11 | molecule_0_10 0.0 0 A 0.00000000 0.00000000 12 | molecule_0_11 0.0 0 A 0.00000000 0.00000000 13 | molecule_0_12 0.0 0 A 0.00000000 0.00000000 14 | molecule_0_13 0.0 0 A 0.00000000 0.00000000 15 | molecule_0_14 0.0 0 A 0.00000000 0.00000000 16 | molecule_0_15 0.0 0 A 0.00000000 0.00000000 17 | molecule_0_16 0.0 0 A 0.00000000 0.00000000 18 | molecule_0_17 0.0 0 A 0.00000000 0.00000000 19 | molecule_0_18 0.0 0 A 0.00000000 0.00000000 20 | molecule_0_19 0.0 0 A 0.00000000 0.00000000 21 | molecule_0_20 0.0 0 A 0.00000000 0.00000000 22 | molecule_0_21 0.0 0 A 0.00000000 0.00000000 23 | molecule_0_22 0.0 0 A 0.00000000 0.00000000 24 | molecule_0_23 0.0 0 A 0.00000000 0.00000000 25 | molecule_0_24 0.0 0 A 0.00000000 0.00000000 26 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # Original PDB CODE: 3LZT 4 | # Structure from X-ray crystallography experiment. 5 | # Select atoms with occupancy higuer than 0.5 6 | 7 | ### TEST: 8 | 9 | # -ff martini 30 open beta 10 | # -scfix and elastic 11 | # adding specific cys bridge as CONECT records 12 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/citation: -------------------------------------------------------------------------------- 1 | Souza, P C T; Marrink, S J; 2020 2 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -x cg.pdb 4 | -o topol.top 5 | -ff martini30b32 6 | -elastic 7 | -cys auto 8 | -dssp 9 | -ignore HOH 10 | -ef 500 -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme/martinize2/topol.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # Original PDB CODE: 3LZT 4 | # Structure from X-ray crystallography experiment. 5 | # Select atoms with occupancy higuer than 0.5 6 | 7 | ### TEST: 8 | 9 | # -ff martini 3001 10 | # -scfix, EN and BB-W bias 11 | # adding specific cys bridge as CONECT records 12 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/citation: -------------------------------------------------------------------------------- 1 | Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 2 | Souza, P C T; Araujo, L P B; Brasnett, C; Moreira, R A; Grunewald, F; Park, P; Wang, L; Razmazma, H; Borges-Araujo, A C; Cofas-Vargas, L F; Monticelli, L; Mera-Adasme, R; Melo, M N; Wu, S; Marrink, S J; Poma, A B; Thallmair, S; Nature Communications 2025; 10.1038/s41467-025-58719-0 -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -ff martini3001 4 | -x cg.pdb 5 | -o topol.top 6 | -ignore HOH 7 | -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC 8 | -elastic 9 | -ef 700 10 | -eu 0.85 11 | -water-bias 12 | -water-bias-eps E:-.5 C:1.0 H:-1.0 13 | -noscfix 14 | -cys none 15 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_ENbias/martinize2/topol.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | 4 | #include "virtual_sites_atomtypes.itp" 5 | #include "virtual_sites_nonbond_params.itp" 6 | #include "molecule_0.itp" 7 | 8 | [ system ] 9 | Title of the system 10 | 11 | [ molecules ] 12 | molecule_0 1 13 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # Original PDB CODE: 3LZT 4 | # Structure from X-ray crystallography experiment. 5 | # Select atoms with occupancy higuer than 0.5 6 | 7 | ### TEST: 8 | 9 | # -ff martini 3001 10 | # -scfix and GO 11 | # adding specific cys bridge as CONECT records 12 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/citation: -------------------------------------------------------------------------------- 1 | Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 2 | Souza, P C T; Araujo, L P B; Brasnett, C; Moreira, R A; Grunewald, F; Park, P; Wang, L; Razmazma, H; Borges-Araujo, A C; Cofas-Vargas, L F; Monticelli, L; Mera-Adasme, R; Melo, M N; Wu, S; Marrink, S J; Poma, A B; Thallmair, S; Nature Communications 2025; 10.1038/s41467-025-58719-0 3 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -ff martini3001 4 | -x cg.pdb 5 | -o topol.top 6 | -ignore HOH 7 | -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC 8 | -go ../map.map 9 | -noscfix 10 | -cys none 11 | -name molecule_0 -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO/martinize2/topol.top: -------------------------------------------------------------------------------- 1 | #define GO_VIRT 2 | #include "martini.itp" 3 | 4 | #include "go_atomtypes.itp" 5 | #include "go_nbparams.itp" 6 | #include "molecule_0.itp" 7 | 8 | [ system ] 9 | Title of the system 10 | 11 | [ molecules ] 12 | molecule_0 1 13 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # Original PDB CODE: 3LZT 4 | # Structure from X-ray crystallography experiment. 5 | # Select atoms with occupancy higuer than 0.5 6 | 7 | ### TEST: 8 | 9 | # -ff martini 3001 10 | # internal go map calculation -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/citation: -------------------------------------------------------------------------------- 1 | Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 2 | Souza, P C T; Araujo, L P B; Brasnett, C; Moreira, R A; Grunewald, F; Park, P; Wang, L; Razmazma, H; Borges-Araujo, A C; Cofas-Vargas, L F; Monticelli, L; Mera-Adasme, R; Melo, M N; Wu, S; Marrink, S J; Poma, A B; Thallmair, S; Nature Communications 2025; 10.1038/s41467-025-58719-0 3 | McGibbon, R T; Beauchamp, K A; Harrigan, M P; Klein, C; Swails, J M; Hernández, C X; Schwantes, C R; Wang, L; Lane, T J; Pande, V S; Biophysical Journal 2015; 10.1016/j.bpj.2015.08.015 4 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -ff martini3001 4 | -x cg.pdb 5 | -o topol.top 6 | -ignore HOH 7 | -dssp 8 | -go 9 | -go-write-file martinize_contact_map.out 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GO_internal/martinize2/topol.top: -------------------------------------------------------------------------------- 1 | #define GO_VIRT 2 | #include "martini.itp" 3 | #include "molecule.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # Original PDB CODE: 3LZT 4 | # Structure from X-ray crystallography experiment. 5 | # Select atoms with occupancy higuer than 0.5 6 | 7 | ### TEST: 8 | 9 | # -ff martini 3001 10 | # -scfix, GO and BB-W bias 11 | # adding specific cys bridge as CONECT records 12 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/citation: -------------------------------------------------------------------------------- 1 | Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 2 | Souza, P C T; Araujo, L P B; Brasnett, C; Moreira, R A; Grunewald, F; Park, P; Wang, L; Razmazma, H; Borges-Araujo, A C; Cofas-Vargas, L F; Monticelli, L; Mera-Adasme, R; Melo, M N; Wu, S; Marrink, S J; Poma, A B; Thallmair, S; Nature Communications 2025; 10.1038/s41467-025-58719-0 3 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -ff martini3001 4 | -x cg.pdb 5 | -o topol.top 6 | -ignore HOH 7 | -ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC 8 | -go ../map.map 9 | -water-bias 10 | -water-bias-eps E:-.5 C:1.0 H:-1.0 11 | -noscfix 12 | -cys none 13 | -name molecule_0 -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_GObias/martinize2/topol.top: -------------------------------------------------------------------------------- 1 | #define GO_VIRT 2 | #include "martini.itp" 3 | 4 | #include "go_atomtypes.itp" 5 | #include "go_nbparams.itp" 6 | #include "molecule_0.itp" 7 | 8 | [ system ] 9 | Title of the system 10 | 11 | [ molecules ] 12 | molecule_0 1 13 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # Original PDB CODE: 3LZT 4 | # Structure from X-ray crystallography experiment. 5 | # Select atoms with occupancy higuer than 0.5 6 | 7 | ### TEST: 8 | 9 | # -ff martini 30 open beta 10 | # -scfix and elastic 11 | # adding specific cys bridge as CONECT records 12 | # contains all protonated AAs for the CHARMM FF 13 | # thus makes sure GLUP ASP LYN and the Histidines are 14 | # recognized correctly 15 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/citation: -------------------------------------------------------------------------------- 1 | Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 2 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -x cg.pdb 4 | -o topol.top 5 | -ff martini3001 6 | -elastic 7 | -cys auto 8 | -dssp 9 | -ignore HOH 10 | -ef 500 11 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/martinize2/topol.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/lysozyme_prot/topol.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/README: -------------------------------------------------------------------------------- 1 | ### 2 | This example checks that all non-physiological protonation 3 | states of ASP, GLU, LYS, HIS are detected correctly. It also 4 | checks that the HIS tautomers are correctly identified. 5 | 6 | ## modifications 7 | GLU7 -> protonated 8 | LYS33 -> deprotonated 9 | ASP18 -> protonated 10 | HIS15 -> d-tautomer 11 | ## unmodifed residues as control 12 | LYS96 13 | LYS97 14 | LYS116 15 | GLU35 16 | ASP48 17 | ASP48 18 | ASP52 (... and more) 19 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/cg.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/citation: -------------------------------------------------------------------------------- 1 | Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J; Nature Methods 2021; 10.1038/s41592-021-01098-3 2 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../input.pdb 3 | -x cg.pdb 4 | -o cg.top 5 | -ff martini3001 6 | -elastic 7 | -scfix 8 | -cys auto 9 | -dssp 10 | -from charmm 11 | -resid input 12 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/prot_modf_charmm/martinize2/sys.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/villin/README: -------------------------------------------------------------------------------- 1 | ### DETAILS: 2 | 3 | # Original PDB CODE: 1VII 4 | # Structure from NMR experiment. 5 | # Selected one of the structures and removed the hydrogens 6 | 7 | ### TEST: 8 | 9 | # -ff martini22p 10 | # -mutation in residue 53: from MET to VAL 11 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/villin/martinize2/citation: -------------------------------------------------------------------------------- 1 | Marrink, S J; Risselada, H J; Yefimov, S; Tieleman, D P; De Vries, A H; The journal of physical chemistry B 2007 2 | de Jong, D H; Singh, G; Bennett, W D; Arnarez, C; Wassenaar, T A; Schaefer, L V; Periole, X; Tieleman, D P; Marrink, S J; Journal of chemical theory and computation 2013 3 | Monticelli, L; Kandasamy, S K; Periole, X; Larson, R G; Tieleman, D P; Marrink, S J; Journal of chemical theory and computation 2008 4 | Yesylevskyy, S O; Schaefer, L V; Sengupta, D; Marrink, S J; PLoS Comput Biol 2010 5 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/villin/martinize2/command: -------------------------------------------------------------------------------- 1 | martinize2 2 | -f ../aa.pdb 3 | -x cg.pdb 4 | -o topol.top 5 | -ff martini22p 6 | -mutate A-MET53:VAL 7 | -resid input 8 | -noscfix 9 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/villin/martinize2/screen.output: -------------------------------------------------------------------------------- 1 | INFO - general - Read 1 molecules from PDB file ../aa.pdb 2 | INFO - step - Guessing the bonds. 3 | INFO - general - 1 molecules after guessing bonds 4 | INFO - step - Repairing the graph. 5 | INFO - general - Mutating residue A-MET53 to VAL 6 | INFO - missing-atom - Missing atom VAL53:CG2 7 | INFO - step - Dealing with modifications. 8 | INFO - general - Identified the modifications ['C-ter'] on residues ['PHE76'] 9 | INFO - step - Read input. 10 | INFO - step - Creating the graph at the target resolution. 11 | INFO - general - Applying modification mapping ('C-ter',) 12 | INFO - step - Averaging the coordinates. 13 | INFO - step - Applying the links. 14 | INFO - step - Placing the charge dummies. 15 | INFO - step - Writing output. 16 | INFO - general - The perfect dry martini recipe: drink gin while looking at a picture of the inventor of vermouth. -- (M*A*S*H) 17 | -------------------------------------------------------------------------------- /vermouth/tests/data/integration_tests/tier-1/villin/martinize2/topol.top: -------------------------------------------------------------------------------- 1 | 2 | #include "martini.itp" 3 | #include "molecule_0.itp" 4 | 5 | [ system ] 6 | Title of the system 7 | 8 | [ molecules ] 9 | molecule_0 1 10 | -------------------------------------------------------------------------------- /vermouth/tests/data/mappings/universal-test/martini-test/ser.mapping: -------------------------------------------------------------------------------- 1 | [ block ] 2 | [ from ] 3 | universal-test 4 | [ to ] 5 | martini-test 6 | 7 | [ from blocks ] 8 | SER 9 | 10 | [ to blocks ] 11 | SER 12 | 13 | [ mapping ] 14 | C BB 15 | CA BB 16 | N BB 17 | HN BB 18 | HA BB 19 | ; Sidechain unmapped on purpose 20 | -------------------------------------------------------------------------------- /vermouth/tests/data/mappings/universal-test/pepplane/modifications.mapping: -------------------------------------------------------------------------------- 1 | ; Copyright 2018 University of Groningen 2 | ; 3 | ; Licensed under the Apache License, Version 2.0 (the "License"); 4 | ; you may not use this file except in compliance with the License. 5 | ; You may obtain a copy of the License at 6 | ; 7 | ; http://www.apache.org/licenses/LICENSE-2.0 8 | ; 9 | ; Unless required by applicable law or agreed to in writing, software 10 | ; distributed under the License is distributed on an "AS IS" BASIS, 11 | ; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | ; See the License for the specific language governing permissions and 13 | ; limitations under the License. 14 | 15 | [ modification ] 16 | [ from ] 17 | universal-test 18 | [ to ] 19 | pepplane 20 | [ from blocks ] 21 | C-ter 22 | [ to blocks ] 23 | C-ter 24 | [ mapping ] 25 | C BB 26 | O BB 27 | OXT BB 28 | [ reference atoms ] 29 | BB C 30 | 31 | [ modification ] 32 | [from] 33 | universal-test 34 | [to] 35 | pepplane 36 | [ from blocks] 37 | N-ter 38 | [to blocks] 39 | N-ter 40 | [mapping] 41 | CA CA 42 | N CA 43 | HN CA 0 44 | HN2 CA 0 45 | HN3 CA 0 46 | [ reference atoms ] 47 | CA CA 48 | -------------------------------------------------------------------------------- /vermouth/tests/data/test_molecule_contacts.out: -------------------------------------------------------------------------------- 1 | Go contact map calculated with vermouth 0.12.1.dev27 2 | 3 | Residue-Residue Contacts 4 | 5 | ID - atom identification 6 | I1,I2 - serial residue id 7 | AA - 3-letter code of aminoacid 8 | C - chain 9 | I(PDB) - residue number in PDB file 10 | DCA - distance between CA 11 | CMs - OV , CSU , oCSU , rCSU 12 | (CSU does not take into account chemical properties of atoms) 13 | rCSU - net contact from rCSU 14 | Count - number of contacts between residues 15 | 16 | ID I1 AA C I(PDB) I2 AA C I(PDB) DCA CMs rCSU Count 17 | ======================================================================================= 18 | R 1 1 res0 A 1 2 res1 A 2 55.9017 0 1 0 0 0 66 19 | R 2 2 res1 A 2 1 res0 A 1 55.9017 0 1 0 0 0 227 20 | R 3 2 res1 A 2 3 res2 A 3 55.9017 0 1 0 0 0 146 21 | R 4 3 res2 A 3 2 res1 A 2 55.9017 0 1 0 0 0 227 22 | R 5 3 res2 A 3 4 res0 A 4 70.7107 0 1 0 0 0 226 23 | R 6 4 res0 A 4 3 res2 A 3 70.7107 0 1 0 0 0 227 24 | -------------------------------------------------------------------------------- /vermouth/tests/integration_tests/__init__.py: -------------------------------------------------------------------------------- 1 | # Copyright 2018 University of Groningen 2 | # 3 | # Licensed under the Apache License, Version 2.0 (the "License"); 4 | # you may not use this file except in compliance with the License. 5 | # You may obtain a copy of the License at 6 | # 7 | # http://www.apache.org/licenses/LICENSE-2.0 8 | # 9 | # Unless required by applicable law or agreed to in writing, software 10 | # distributed under the License is distributed on an "AS IS" BASIS, 11 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | # See the License for the specific language governing permissions and 13 | # limitations under the License. 14 | -------------------------------------------------------------------------------- /vermouth/tests/test_cif_reader.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # Copyright 2025 University of Groningen 3 | # 4 | # Licensed under the Apache License, Version 2.0 (the "License"); 5 | # you may not use this file except in compliance with the License. 6 | # You may obtain a copy of the License at 7 | # 8 | # http://www.apache.org/licenses/LICENSE-2.0 9 | # 10 | # Unless required by applicable law or agreed to in writing, software 11 | # distributed under the License is distributed on an "AS IS" BASIS, 12 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 13 | # See the License for the specific language governing permissions and 14 | # limitations under the License. 15 | 16 | """ 17 | Unittests for the CIF reader. 18 | """ 19 | 20 | import vermouth 21 | from vermouth import CIFInput 22 | from vermouth.tests.datafiles import CIF_PROTEIN 23 | 24 | def test_CIFInput(): 25 | 26 | system = vermouth.System() 27 | CIFInput(filename=CIF_PROTEIN, exclude='HOH', ignh=False, modelidx=1).run_system(system) 28 | 29 | assert len(system.molecules) == 1 30 | -------------------------------------------------------------------------------- /vermouth/tests/test_version.py: -------------------------------------------------------------------------------- 1 | # Copyright 2018 University of Groningen 2 | # 3 | # Licensed under the Apache License, Version 2.0 (the "License"); 4 | # you may not use this file except in compliance with the License. 5 | # You may obtain a copy of the License at 6 | # 7 | # http://www.apache.org/licenses/LICENSE-2.0 8 | # 9 | # Unless required by applicable law or agreed to in writing, software 10 | # distributed under the License is distributed on an "AS IS" BASIS, 11 | # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 12 | # See the License for the specific language governing permissions and 13 | # limitations under the License. 14 | 15 | import vermouth 16 | 17 | 18 | def test_version(): 19 | assert isinstance(vermouth.__version__, str) 20 | --------------------------------------------------------------------------------