├── .gitignore ├── README.md ├── amber14sb_OL15.ff ├── Makefile.am ├── Makefile.in ├── README.md ├── aminoacids.arn ├── aminoacids.c.tdb ├── aminoacids.hdb ├── aminoacids.n.tdb ├── aminoacids.r2b ├── aminoacids.rtp ├── aminoacids.vsd ├── atomtypes.atp ├── dna.arn ├── dna.hdb ├── dna.r2b ├── dna.rtp ├── ffbonded.itp ├── ffnonbonded.itp ├── forcefield.doc ├── forcefield.itp ├── gbsa.itp ├── ions.itp ├── rna.arn ├── rna.hdb ├── rna.r2b ├── rna.rtp ├── spc.itp ├── spce.itp ├── tip3p.itp ├── tip4p.itp ├── tip4pew.itp ├── tip5p.itp ├── urea.itp └── watermodels.dat ├── amber14sb_OL15_cufix_zn.ff ├── #crw.itp.1# ├── #crw.itp.2# ├── Makefile.am ├── Makefile.in ├── SI │ ├── README │ ├── aminoacids.hdb │ ├── aminoacids.rtp │ ├── atomtypes.atp │ ├── ffbonded.itp │ ├── ffnonbonded.itp │ └── residuetypes.dat ├── aminoacids.arn ├── aminoacids.c.tdb ├── aminoacids.hdb ├── aminoacids.n.tdb ├── aminoacids.r2b ├── aminoacids.rtp ├── aminoacids.vsd ├── atomtypes.atp ├── atomtypes.atp~ ├── crw.itp ├── cufix.itp ├── dna.arn ├── dna.hdb ├── dna.r2b ├── dna.rtp ├── dna.rtp~ ├── ffbonded.itp ├── ffbonded.itp~ ├── ffnonbonded.itp ├── ffnonbonded.itp~ ├── forcefield.doc ├── forcefield.doc~ ├── forcefield.itp ├── forcefield.itp~ ├── gbsa.itp ├── ions.itp ├── rna.arn ├── rna.hdb ├── rna.r2b ├── rna.rtp ├── rna.rtp~ ├── spc.itp ├── spce.itp ├── tip3p.itp ├── tip4p.itp ├── tip4pew.itp ├── tip5p.itp ├── urea.itp └── watermodels.dat ├── amber14sb_parmbsc1.ff ├── Makefile.am ├── Makefile.in ├── README.md ├── aminoacids.arn ├── aminoacids.c.tdb ├── aminoacids.hdb ├── aminoacids.n.tdb ├── aminoacids.r2b ├── aminoacids.rtp ├── aminoacids.vsd ├── atomtypes.atp ├── dna.arn ├── dna.hdb ├── dna.r2b ├── dna.rtp ├── ffbonded.itp ├── ffnonbonded.itp ├── forcefield.doc ├── forcefield.itp ├── gbsa.itp ├── ions.itp ├── rna.arn ├── rna.hdb ├── rna.r2b ├── rna.rtp ├── spc.itp ├── spce.itp ├── tip3p.itp ├── tip4p.itp ├── tip4pew.itp ├── tip5p.itp ├── urea.itp └── watermodels.dat ├── amber14sb_parmbsc1_cufix.ff ├── Makefile.am ├── Makefile.in ├── README.md ├── aminoacids.arn ├── aminoacids.c.tdb ├── aminoacids.hdb ├── aminoacids.n.tdb ├── aminoacids.r2b ├── aminoacids.rtp ├── aminoacids.vsd ├── atomtypes.atp ├── ca-sol7.itp ├── ca-sol7.pdb ├── cufix.itp ├── dna.arn ├── dna.hdb ├── dna.r2b ├── dna.rtp ├── ffbonded.itp ├── ffnonbonded.itp ├── ffnonbonded.itp~ ├── forcefield.doc ├── forcefield.itp ├── forcefield.itp~ ├── gbsa.itp ├── ions.itp ├── mg-sol6.itp ├── mg-sol6.pdb ├── rna.arn ├── rna.hdb ├── rna.r2b ├── rna.rtp ├── spc.itp ├── spce.itp ├── tip3p.itp ├── tip4p.itp ├── tip4pew.itp ├── tip5p.itp ├── urea.itp └── watermodels.dat ├── amber14sb_parmbsc1_cufix_PTM.ff ├── .ipynb_checkpoints │ ├── Makefile-checkpoint.am │ ├── Makefile-checkpoint.in │ ├── PSER-checkpoint.hdb │ ├── PSER-checkpoint.rtp │ ├── PTM-checkpoint.arn │ ├── aminoacids-checkpoint.arn │ ├── aminoacids-checkpoint.hdb │ ├── aminoacids-checkpoint.r2b │ ├── aminoacids-checkpoint.rtp │ ├── aminoacids-checkpoint.vsd │ ├── aminoacids.c-checkpoint.tdb │ ├── aminoacids.n-checkpoint.tdb │ ├── atomtypes-checkpoint.atp │ ├── cufix-checkpoint.itp │ ├── dna-checkpoint.arn │ ├── dna-checkpoint.r2b │ ├── ffbonded-checkpoint.itp │ ├── ffnonbonded-checkpoint.itp │ ├── forcefield-checkpoint.itp │ ├── gbsa-checkpoint.itp │ ├── residuetypes-checkpoint.dat │ └── rna-checkpoint.arn ├── Makefile.am ├── Makefile.in ├── PSER.hdb ├── PSER.rtp ├── PTM.arn ├── README.md ├── aminoacids.arn ├── aminoacids.c.tdb ├── aminoacids.hdb ├── aminoacids.n.tdb ├── aminoacids.r2b ├── aminoacids.rtp ├── aminoacids.vsd ├── atomtypes.atp ├── ca-sol7.itp ├── ca-sol7.pdb ├── cufix.itp ├── dna.arn ├── dna.hdb ├── dna.r2b ├── dna.rtp ├── ffbonded.itp ├── ffnonbonded.itp ├── ffnonbonded.itp~ ├── forcefield.doc ├── forcefield.itp ├── forcefield.itp~ ├── gbsa.itp ├── ions.itp ├── mg-sol6.itp ├── mg-sol6.pdb ├── residuetypes.dat ├── rna.arn ├── rna.hdb ├── rna.r2b ├── rna.rtp ├── spc.itp ├── spce.itp ├── tip3p.itp ├── tip4p.itp ├── tip4pew.itp ├── tip5p.itp ├── urea.itp └── watermodels.dat ├── amber14sb_parmbsc1_opc_lmi.ff ├── Makefile.am ├── Makefile.in ├── README.md ├── aminoacids.arn ├── aminoacids.c.tdb ├── aminoacids.hdb ├── aminoacids.n.tdb ├── aminoacids.r2b ├── aminoacids.rtp ├── aminoacids.vsd ├── atomtypes.atp ├── dna.arn ├── dna.hdb ├── dna.r2b ├── dna.rtp ├── ffbonded.itp ├── ffnonbonded.itp ├── forcefield.doc ├── forcefield.itp ├── frcmod.ions1lm_126_hfe_opc ├── frcmod.ionsjc_tip3p ├── gbsa.itp ├── ions.itp ├── opc.itp ├── rna.arn ├── rna.hdb ├── rna.r2b ├── rna.rtp ├── spc.itp ├── spce.itp ├── tip3p.itp ├── tip4p.itp ├── tip4pew.itp ├── tip5p.itp ├── urea.itp └── watermodels.dat ├── amber14sb_parmbsc1_opc_lmi_PTM.ff ├── .ipynb_checkpoints │ ├── Makefile-checkpoint.am │ ├── PSER-checkpoint.rtp │ ├── aminoacids-checkpoint.r2b │ ├── aminoacids-checkpoint.rtp │ ├── ffbonded-checkpoint.itp │ └── residuetypes-checkpoint.dat ├── Makefile.am ├── Makefile.in ├── PSER.hdb ├── PSER.rtp ├── README.md ├── aminoacids.arn ├── aminoacids.c.tdb ├── aminoacids.hdb ├── aminoacids.n.tdb ├── aminoacids.r2b ├── aminoacids.rtp ├── aminoacids.vsd ├── atomtypes.atp ├── dna.arn ├── dna.hdb ├── dna.r2b ├── dna.rtp ├── ffbonded.itp ├── ffnonbonded.itp ├── forcefield.doc ├── forcefield.itp ├── frcmod.ions1lm_126_hfe_opc ├── frcmod.ionsjc_tip3p ├── gbsa.itp ├── ions.itp ├── opc.itp ├── residuetypes.dat ├── rna.arn ├── rna.hdb ├── rna.r2b ├── rna.rtp ├── spc.itp ├── spce.itp ├── tip3p.itp ├── tip4p.itp ├── tip4pew.itp ├── tip5p.itp ├── urea.itp └── watermodels.dat ├── amber19sb_parmbsc1_opc.ff ├── amb2gro_top_gro_cmap.py ├── build_box_prod.sh ├── cpptraj_strip_solvent.in └── tleap_draft_box.rc ├── amber99bsc1.ff ├── README.md ├── aminoacids.arn ├── aminoacids.c.tdb ├── aminoacids.hdb ├── aminoacids.n.tdb ├── aminoacids.r2b ├── aminoacids.rtp ├── aminoacids.vsd ├── atomtypes.atp ├── dna.arn ├── dna.hdb ├── dna.r2b ├── dna.rtp ├── ffbonded.itp ├── ffnonbonded.itp ├── forcefield.doc ├── forcefield.itp ├── gbsa.itp ├── ions.itp ├── rna.arn ├── rna.hdb ├── rna.r2b ├── rna.rtp ├── spc.itp ├── spce.itp ├── tip3p.itp ├── tip4p.itp ├── tip4pew.itp ├── tip5p.itp ├── urea.itp └── watermodels.dat ├── charmm36-mar2019.ff ├── README.md ├── atomtypes.atp ├── cmap.itp ├── ffbonded.itp ├── ffnonbonded.itp ├── forcefield.doc ├── forcefield.itp ├── gb.itp ├── ions.itp ├── merged.arn ├── merged.c.tdb ├── merged.hdb ├── merged.n.tdb ├── merged.r2b ├── merged.rtp ├── merged.vsd ├── nbfix.itp ├── old_c36_cmap.itp ├── spc.itp ├── spce.itp ├── tip3p.itp ├── tip4p.itp ├── toppar_c36_jul18 │ ├── 00toppar_file_format.txt │ ├── par_all22_prot.prm │ ├── par_all35_ethers.prm │ ├── par_all36_carb.prm │ ├── par_all36_cgenff.prm │ ├── par_all36_lipid.prm │ ├── par_all36_na.prm │ ├── par_all36_prot.prm │ ├── par_all36m_prot.prm │ ├── par_hbond.inp │ ├── param19.inp │ ├── top_all22_prot.rtf │ ├── top_all35_ethers.rtf │ ├── top_all36_carb.rtf │ ├── top_all36_cgenff.rtf │ ├── top_all36_lipid.rtf │ ├── top_all36_na.rtf │ ├── top_all36_prot.rtf │ ├── toph19.inp │ ├── toppar_all.history │ └── toppar_water_ions.str └── watermodels.dat ├── charmm36-mar2019_cufix.ff ├── README.md ├── atomtypes.atp ├── cmap.itp ├── convert_cufix.py ├── ffbonded.itp ├── ffnonbonded.itp ├── forcefield.doc ├── forcefield.itp ├── gb.itp ├── ions.itp ├── merged.arn ├── merged.c.tdb ├── merged.hdb ├── merged.n.tdb ├── merged.r2b ├── merged.rtp ├── merged.vsd ├── nbfix.itp ├── old_c36_cmap.itp ├── spc.itp ├── spce.itp ├── tip3p.itp ├── tip4p.itp ├── toppar_c36_jul18 │ ├── 00toppar_file_format.txt │ ├── par_all22_prot.prm │ ├── par_all35_ethers.prm │ ├── par_all36_carb.prm │ ├── par_all36_cgenff.prm │ ├── par_all36_lipid.prm │ ├── par_all36_na.prm │ ├── par_all36_prot.prm │ ├── par_all36m_prot.prm │ ├── par_hbond.inp │ ├── param19.inp │ ├── top_all22_prot.rtf │ ├── top_all35_ethers.rtf │ ├── top_all36_carb.rtf │ ├── top_all36_cgenff.rtf │ ├── top_all36_lipid.rtf │ ├── top_all36_na.rtf │ ├── top_all36_prot.rtf │ ├── toph19.inp │ ├── 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