├── .gitignore ├── .readthedocs.yaml ├── LICENSE ├── README.md ├── bin ├── CombineMartini.py ├── backmap.py ├── calDihedral.py ├── checkstructure.py ├── convert.py ├── dms-dump.py ├── dump.py ├── loopmodeler.py ├── map.py ├── minimize.py ├── plot.py └── timeseries2animation.py ├── data ├── DLPC1_283K.csv ├── DLPC1_303K.csv ├── DLPC1_323K.csv ├── DLPC2_283K.csv ├── DLPC2_303K.csv ├── DLPC2_323K.csv ├── DPPC1_323K.csv ├── DPPC2_323K.csv ├── DPPC2_323K_Douliez.csv ├── Ferreria_POPC1.csv ├── Ferreria_POPC2.csv ├── POPE1.csv ├── POPE2.csv └── README ├── docs ├── Makefile ├── README.md ├── make.bat ├── requirements.txt └── source │ ├── POPC.afdesign │ ├── backmap.rst │ ├── bilayer.afdesign │ ├── bilayer.png │ ├── conf.py │ ├── consistency.afdesign │ ├── consistency.png │ ├── ethane.afdesign │ ├── ethane.png │ ├── index.rst │ ├── input.rst │ ├── installation.rst │ ├── isomer.afdesign │ ├── isomer.png │ ├── lipids.png │ ├── membranebuilder.rst │ ├── methane.afdesign │ ├── methane.png │ ├── mscgbackmapping.rst │ └── popc.png ├── install.sh ├── notes_to_myself.txt ├── pyproject.toml ├── requirements.txt ├── setup.py ├── src └── mstool │ ├── FF │ ├── amber14 │ │ ├── DNA.OL15.xml │ │ ├── DNA.bsc1.xml │ │ ├── RNA.OL3.xml │ │ ├── amber14-all.xml │ │ ├── lipid17.xml │ │ ├── protein.ff14SB.xml │ │ ├── protein.ff15ipq.xml │ │ ├── spce.xml │ │ ├── tip3p.xml │ │ ├── tip3pfb.xml │ │ ├── tip4pew.xml │ │ └── tip4pfb.xml │ ├── amber99 │ │ ├── amber99sbildn.xml │ │ └── tip3p.xml │ ├── charmm36.toppar │ │ ├── toppar.lipid.str │ │ ├── toppar.str │ │ └── toppar │ │ │ ├── cam.str │ │ │ ├── mass.str │ │ │ ├── par_all36_carb.prm │ │ │ ├── par_all36_cgenff.prm │ │ │ ├── par_all36_lipid.prm │ │ │ ├── par_all36_na.prm │ │ │ ├── par_all36m_prot.prm │ │ │ ├── par_interface.prm │ │ │ ├── tip216.crd │ │ │ ├── top_all36_carb.rtf │ │ │ ├── top_all36_cgenff.rtf │ │ │ ├── top_all36_lipid.rtf │ │ │ ├── top_all36_na.rtf │ │ │ ├── top_all36_prot.rtf │ │ │ ├── top_interface.rtf │ │ │ ├── toppar_all36_carb_glycolipid.str │ │ │ ├── toppar_all36_carb_glycopeptide.str │ │ │ ├── toppar_all36_carb_imlab.str │ │ │ ├── toppar_all36_label_fluorophore.str │ │ │ ├── toppar_all36_label_spin.str │ │ │ ├── toppar_all36_lipid_archaeal.str │ │ │ ├── toppar_all36_lipid_bacterial.str │ │ │ ├── toppar_all36_lipid_cardiolipin.str │ │ │ ├── toppar_all36_lipid_cholesterol.str │ │ │ ├── toppar_all36_lipid_dag.str │ │ │ ├── toppar_all36_lipid_detergent.str │ │ │ ├── toppar_all36_lipid_ether.str │ │ │ ├── toppar_all36_lipid_hmmm.str │ │ │ ├── toppar_all36_lipid_inositol.str │ │ │ ├── toppar_all36_lipid_lnp.str │ │ │ ├── toppar_all36_lipid_lps.str │ │ │ ├── toppar_all36_lipid_miscellaneous.str │ │ │ ├── toppar_all36_lipid_model.str │ │ │ ├── toppar_all36_lipid_mycobacterial.str │ │ │ ├── toppar_all36_lipid_oxidized.str │ │ │ ├── toppar_all36_lipid_prot.str │ │ │ ├── toppar_all36_lipid_sphingo.str │ │ │ ├── toppar_all36_lipid_tag.str │ │ │ ├── toppar_all36_lipid_yeast.str │ │ │ ├── toppar_all36_moreions.str │ │ │ ├── toppar_all36_na_nad_ppi.str │ │ │ ├── toppar_all36_na_rna_modified.str │ │ │ ├── toppar_all36_nano_lig.str │ │ │ ├── toppar_all36_nano_lig_patch.str │ │ │ ├── toppar_all36_polymer_solvent.str │ │ │ ├── toppar_all36_prot_arg0.str │ │ │ ├── toppar_all36_prot_c36m_d_aminoacids.str │ │ │ ├── toppar_all36_prot_fluoro_alkanes.str │ │ │ ├── toppar_all36_prot_heme.str │ │ │ ├── toppar_all36_prot_model.str │ │ │ ├── toppar_all36_prot_modify_res.str │ │ │ ├── toppar_all36_prot_na_combined.str │ │ │ ├── toppar_all36_prot_retinol.str │ │ │ ├── toppar_all36_synthetic_polymer.str │ │ │ ├── toppar_all36_synthetic_polymer_patch.str │ │ │ ├── toppar_dum_noble_gases.str │ │ │ ├── toppar_ions_won.str │ │ │ └── toppar_water_ions.str │ ├── charmm36 │ │ ├── charmm36.initial.xml │ │ ├── charmm36.xml │ │ ├── chyo.xml │ │ ├── clol.xml │ │ ├── mdps │ │ │ ├── step5.mdp │ │ │ ├── step6.mdp │ │ │ └── step7.mdp │ │ ├── pip.xml │ │ ├── triv.xml │ │ └── water.xml │ ├── martini2.2 │ │ ├── martini_lipids_add.itp │ │ ├── martini_v2.0_ions.itp │ │ ├── martini_v2.0_lipids_all_201506.itp │ │ ├── martini_v2.2.itp │ │ ├── martini_v2.2.modified.LJ.itp │ │ ├── martini_v2.2.modified.itp │ │ ├── martini_v2.2_proteins │ │ │ ├── ALA │ │ │ │ ├── ALA.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── ARG │ │ │ │ ├── ARG.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── ASN │ │ │ │ ├── ASN.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── ASP │ │ │ │ ├── ASP.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── CYS │ │ │ │ ├── CYS.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── GLN │ │ │ │ ├── GLN.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── GLU │ │ │ │ ├── GLU.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── GLY │ │ │ │ ├── GLY.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── HIE │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── HIS │ │ │ │ ├── HIS.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── ILE │ │ │ │ ├── ILE.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── LEU │ │ │ │ ├── LEU.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── LYS │ │ │ │ ├── LYS.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── MET │ │ │ │ ├── MET.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── PHE │ │ │ │ ├── PHE.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── PRO │ │ │ │ ├── PRO.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── SER │ │ │ │ ├── SER.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── THR │ │ │ │ ├── THR.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── TRP │ │ │ │ ├── TRP.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── TYR │ │ │ │ ├── TYR.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── VAL │ │ │ │ ├── VAL.itp │ │ │ │ ├── input.pdb │ │ │ │ └── input_cg.pdb │ │ │ ├── martinize_v2.6.py │ │ │ ├── protein.gro │ │ │ ├── proteins.itp │ │ │ ├── proteins_HIS.itp │ │ │ └── run_martinize.sh │ │ ├── martinize.py │ │ ├── martinize_v2.5.py │ │ ├── martinize_v2.6.py │ │ ├── mdps │ │ │ ├── step4.mdp │ │ │ ├── step5.0.mdp │ │ │ ├── step5.1.mdp │ │ │ ├── step5.2.mdp │ │ │ └── step6.mdp │ │ ├── nonbond_params │ │ ├── nonbond_params.py │ │ ├── nonbond_params_LJ │ │ ├── structures │ │ │ ├── CHL1.pdb │ │ │ ├── CHOL.pdb │ │ │ ├── P005.itp │ │ │ ├── P005.pdb │ │ │ ├── P006.itp │ │ │ ├── P006.pdb │ │ │ ├── P007.itp │ │ │ ├── P007.pdb │ │ │ ├── P008.itp │ │ │ ├── P008.pdb │ │ │ ├── P010.itp │ │ │ ├── P010.pdb │ │ │ ├── chol_test │ │ │ │ ├── chol.EM.pdb │ │ │ │ ├── chol.EM2.pdb │ │ │ │ ├── chol.martini.dms │ │ │ │ ├── chol.martini2.dms │ │ │ │ ├── run.py │ │ │ │ └── topol.top │ │ │ ├── makepore.py │ │ │ └── waterpore_test │ │ │ │ ├── P008.EM.dms │ │ │ │ ├── P008.dms │ │ │ │ ├── P008.itp │ │ │ │ ├── P008.pdb │ │ │ │ ├── run.py │ │ │ │ └── topol.top │ │ ├── ti.itp │ │ ├── toy.itp │ │ └── tp.itp │ └── martini3.0.0 │ │ ├── lipids.itp │ │ ├── martini.itp │ │ ├── martini_v3.0.0.itp │ │ ├── martini_v3.0.0_ions_v1.itp │ │ ├── martini_v3.0.0_nucleobases_v1.itp │ │ ├── martini_v3.0.0_phospholipids_v1.itp │ │ ├── martini_v3.0.0_phospholipids_v1_matthieu.itp │ │ ├── martini_v3.0.0_small_molecules_v1.itp │ │ ├── martini_v3.0.0_solvents_v1.itp │ │ ├── martini_v3.0.0_sugars_v1.itp │ │ ├── martini_v3.0.b.3.2.itp │ │ ├── martini_v3.0_sterols_v1.0.itp │ │ ├── mdps │ │ ├── mdout.mdp │ │ ├── run.sh │ │ ├── step6.0.mdp │ │ ├── step6.1.mdp │ │ ├── step6.2.mdp │ │ ├── step6.3.mdp │ │ ├── step6.4.mdp │ │ ├── step6.5.mdp │ │ ├── step6.6.mdp │ │ └── step7.mdp │ │ ├── phospholipids.itp │ │ └── protein.itp │ ├── __init__.py │ ├── authors.py │ ├── backup │ ├── 4xnv.pdb │ ├── amberselection_20240510.py │ ├── backmap.py │ ├── bilayer_240429.py │ ├── bilayerbuilder_240429.py │ ├── cg2aa │ │ ├── cg2aa.py │ │ └── ompfcg.pdb │ ├── fill.bck.py │ ├── fill_loops.py │ ├── fill_side.py │ ├── gmx2dms2.py │ ├── loopmodeler_230719.py │ ├── martinizedms.231213.py │ ├── martinizedms.240309.py │ ├── openmmutils_230719.py │ ├── orient_240621.py │ ├── pandas2dict.py │ ├── rem.bck.py │ ├── rem_230719.py │ ├── rem_230801.py │ ├── rock_240306.py │ ├── sphere_240304.py │ ├── ungroup.py │ ├── ungroup_240430.py │ ├── universe_20240510.py │ └── universe_20240511.py │ ├── core │ ├── __init__.py │ ├── backmap.py │ ├── calSolv.py │ ├── checkff.py │ ├── checkstructure.py │ ├── checktetrahedron.py │ ├── divideconquer.py │ ├── dms2openmm.py │ ├── dmsfile.py │ ├── fill.py │ ├── gmx2dms.py │ ├── loopmodeler.py │ ├── map.py │ ├── martinizedms.py │ ├── mutate.py │ ├── orient.py │ ├── readmappings.py │ ├── readmartini.py │ ├── readtoppars.py │ ├── readxml.py │ ├── rem.py │ ├── reorderatoms.py │ ├── seq.py │ ├── solvate_martini.py │ ├── truncateprotein.py │ ├── ungroup.py │ └── universe.py │ ├── examples │ ├── Backmapping │ │ ├── Example1_methane │ │ │ ├── cg.pdb │ │ │ ├── ff.xml │ │ │ ├── mapping.dat │ │ │ ├── run.py │ │ │ └── vis.cxc │ │ ├── Example2_ethane │ │ │ ├── cg.pdb │ │ │ ├── mapping.dat │ │ │ ├── run.py │ │ │ └── vis.cxc │ │ ├── Example3_butene │ │ │ ├── cg.pdb │ │ │ ├── ff.xml │ │ │ ├── mapping.dat │ │ │ └── run.py │ │ ├── Example4_POPC │ │ │ ├── cg.pdb │ │ │ └── run.py │ │ ├── Example5_Sphere │ │ │ └── cg.pdb │ │ ├── Example6_TRIO │ │ │ ├── cg.pdb │ │ │ ├── ff.xml │ │ │ ├── mapping.5.dat │ │ │ ├── mapping.dat │ │ │ ├── martini.5.itp │ │ │ ├── martini.itp │ │ │ ├── run.py │ │ │ └── setup.py │ │ ├── Example7_MembraneProtein │ │ │ ├── cg.pdb │ │ │ ├── cg_nonprotein.pdb │ │ │ ├── protein_AA.pdb │ │ │ ├── protein_AA2.pdb │ │ │ └── run.py │ │ └── run_all.py │ ├── BackmappingMartini3 │ │ ├── README.md │ │ ├── b2ar_mix8.gro │ │ ├── curved.gro │ │ ├── ff.xml │ │ ├── mapping.dat │ │ ├── mix8_3017lipids.gro │ │ ├── mix8_419lipids.gro │ │ ├── mix8_5111lipids.gro │ │ └── run.py │ ├── BilayerBuilder │ │ ├── 3sn6.pdb │ │ ├── 4xnv.pdb │ │ ├── 6ds5.pdb │ │ ├── gpcr │ │ │ ├── 3sn6.pdb │ │ │ ├── README │ │ │ ├── ROCK.xml │ │ │ ├── gpcr.png │ │ │ ├── run.py │ │ │ └── seq.fasta │ │ ├── run_all.py │ │ ├── run_martini3.py │ │ ├── sars │ │ │ ├── E5.pdb │ │ │ ├── M2.pdb │ │ │ ├── S3.pdb │ │ │ └── run.py │ │ ├── sars_small │ │ │ ├── E5.pdb │ │ │ ├── M2.pdb │ │ │ ├── S3.pdb │ │ │ ├── S3.protein.pdb │ │ │ └── run.py │ │ ├── showhalf.py │ │ └── vis.cxc │ ├── Disulfide │ │ └── 9DYP │ │ │ ├── 9DYP.pdb │ │ │ ├── 9DYP_CG.pdb │ │ │ └── run.py │ └── NucleicAcid │ │ ├── 1BNA │ │ ├── 1BNA.pdb │ │ ├── 1BNA_CG.pdb │ │ └── run.py │ │ ├── 1J46 │ │ ├── 1J46.pdb │ │ ├── 1J46_CG.pdb │ │ └── run.py │ │ ├── 1RNA │ │ ├── 1RNA.pdb │ │ ├── 1RNA_CG.pdb │ │ └── run.py │ │ └── 8YYV │ │ ├── 8YYV.pdb │ │ ├── 8YYV_CG.pdb │ │ └── run.py │ ├── lib │ ├── align.py │ ├── distance.memory.py │ ├── distance.py │ ├── distance_matrix.ipynb │ ├── distancelib.pyx │ ├── qcprot.pyx │ └── setup.py │ ├── mapping │ ├── lipids.afdesign │ ├── lipids.png │ ├── martini.amber14.dat │ ├── martini.lipid.c36.dat │ ├── martini.na.c36.dat │ ├── martini.protein.c36m.dat │ ├── martini3.protein.c36m.dat │ ├── protein.afdesign │ ├── protein.png │ └── structures │ │ ├── CHL1.pdb │ │ ├── CHL1_AA.pdb │ │ ├── CHYO.bck.pdb │ │ ├── CHYO.pdb │ │ ├── CHYO_AA.bck.pdb │ │ └── CHYO_AA.pdb │ ├── membrane │ ├── bilayer.py │ ├── bilayerbuilder.py │ ├── buildingblock.py │ ├── buildingblock.xml │ ├── lipid.py │ ├── newlipid.py │ ├── sphere.py │ ├── spherebuilder.py │ └── sphereprotein.py │ ├── utils │ ├── __init__.py │ ├── add_termini_atoms.py │ ├── amberselection.py │ ├── atomic_data.py │ ├── cap_termini_residues.py │ ├── change_his.py │ ├── dump.py │ ├── gmx_energy.py │ ├── mdautils.py │ ├── openmmutils.20250701.py │ ├── openmmutils.py │ ├── performance.py │ ├── protein_sel.py │ ├── rock.py │ ├── rockchain.py │ ├── rockresidue.py │ ├── saveargs.py │ ├── sdminimizer.py │ ├── sqlcmd.py │ ├── util.py │ ├── vismol.py │ └── writepsf.py │ └── version.py ├── tests ├── 1RNA_CG.pdb └── test_na.py └── tutorial.pdf /.gitignore: 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