├── .codecov.yml ├── .github └── workflows │ └── codeql-analysis.yml ├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── cg2at ├── conda └── conda_upload.sh ├── database ├── bin │ ├── .gitignore │ ├── at_mod.py │ ├── at_mod_np.py │ ├── at_mod_p.py │ ├── cg2at.py │ ├── check_library.py │ ├── g_var.py │ ├── gen.py │ ├── gro.py │ ├── images │ │ ├── Fragment.png │ │ ├── group_vs_mod.png │ │ ├── hybrid.png │ │ ├── threaded.png │ │ ├── workflow.odg │ │ ├── workflow.png │ │ ├── workflow_short.jpg │ │ ├── workflow_short.odg │ │ └── workflow_short.png │ └── read_in.py ├── forcefields │ ├── README.md │ ├── amber14_lipid17_will_be_removed.ff │ │ ├── Makefile.am │ │ ├── Makefile.in │ │ ├── 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 │ │ ├── lipids.rtp │ │ ├── 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.ff │ │ ├── Makefile.am │ │ ├── Makefile.in │ │ ├── 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.ff │ │ ├── Makefile.am │ │ ├── Makefile.in │ │ ├── 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_OL21.ff │ │ ├── Makefile.am │ │ ├── Makefile.in │ │ ├── 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 │ │ ├── leap.log │ │ ├── rna.arn │ │ ├── rna.hdb │ │ ├── rna.r2b │ │ ├── rna.rtp │ │ ├── spc.itp │ │ ├── spce.itp │ │ ├── tip3p.itp │ │ ├── tip4p.itp │ │ ├── tip4pew.itp │ │ ├── tip5p.itp │ │ ├── urea.itp │ │ └── watermodels.dat │ ├── amber99sb-ildn.ff │ │ ├── Joung_et_al_ion_parameters.pdf │ │ ├── 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 │ ├── amber99sb-ildn_slipids.ff │ │ ├── Joung_et_al_ion_parameters.pdf │ │ ├── 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 │ ├── amber99sb-ildn_slipids_spc.ff │ │ ├── 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 │ ├── amber99sb-ildn_slipids_tip3p.ff │ │ ├── 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 │ ├── amber99sb-ildn_spc.ff │ │ ├── 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 │ ├── amber99sb-ildn_tip3p.ff │ │ ├── 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-jul2020-updated.ff │ │ ├── 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 │ │ └── watermodels.dat │ ├── charmm36-jul2020.ff │ │ ├── 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 │ │ └── watermodels.dat │ ├── charmm36-jul2021.ff │ │ ├── aminoacids.arn │ │ ├── aminoacids.c.tdb │ │ ├── aminoacids.hdb │ │ ├── aminoacids.n.tdb │ │ ├── aminoacids.r2b │ │ ├── aminoacids.rtp │ │ ├── atomtypes.atp │ │ ├── carb.c.tdb │ │ ├── carb.hdb │ │ ├── carb.n.tdb │ │ ├── carb.r2b │ │ ├── carb.rtp │ │ ├── cgenff.c.tdb │ │ ├── cgenff.hdb │ │ ├── cgenff.n.tdb │ │ ├── cgenff.r2b │ │ ├── cgenff.rtp │ │ ├── cmap.itp │ │ ├── ethers.c.tdb │ │ ├── ethers.hdb │ │ ├── ethers.n.tdb │ │ ├── ethers.r2b │ │ ├── ethers.rtp │ │ ├── ffbonded.itp │ │ ├── ffmissingdihedrals.itp │ │ ├── ffnonbonded.itp │ │ ├── forcefield.doc │ │ ├── forcefield.itp │ │ ├── ions.itp │ │ ├── lipid.c.tdb │ │ ├── lipid.hdb │ │ ├── lipid.n.tdb │ │ ├── lipid.r2b │ │ ├── lipid.rtp │ │ ├── metals.c.tdb │ │ ├── metals.hdb │ │ ├── metals.n.tdb │ │ ├── metals.r2b │ │ ├── metals.rtp │ │ ├── na.c.tdb │ │ ├── na.hdb │ │ ├── na.n.tdb │ │ ├── na.r2b │ │ ├── na.rtp │ │ ├── nbfix.itp │ │ ├── silicates.c.tdb │ │ ├── silicates.hdb │ │ ├── silicates.n.tdb │ │ ├── silicates.r2b │ │ ├── silicates.rtp │ │ ├── solvent.c.tdb │ │ ├── solvent.hdb │ │ ├── solvent.n.tdb │ │ ├── solvent.r2b │ │ ├── solvent.rtp │ │ ├── spc.itp │ │ ├── spce.itp │ │ ├── tip3p.itp │ │ ├── tip3p_original.itp │ │ ├── tip4p.itp │ │ ├── tip4pew.itp │ │ ├── tip5p.itp │ │ └── watermodels.dat │ ├── charmm36-jul2022.ff │ │ ├── aminoacids.arn │ │ ├── aminoacids.c.tdb │ │ ├── aminoacids.hdb │ │ ├── aminoacids.n.tdb │ │ ├── aminoacids.r2b │ │ ├── aminoacids.rtp │ │ ├── atomtypes.atp │ │ ├── carb.c.tdb │ │ ├── carb.hdb │ │ ├── carb.n.tdb │ │ ├── carb.r2b │ │ ├── carb.rtp │ │ ├── cgenff.c.tdb │ │ ├── cgenff.hdb │ │ ├── cgenff.n.tdb │ │ ├── cgenff.r2b │ │ ├── cgenff.rtp │ │ ├── cmap.itp │ │ ├── ethers.c.tdb │ │ ├── ethers.hdb │ │ ├── ethers.n.tdb │ │ ├── ethers.r2b │ │ ├── ethers.rtp │ │ ├── ffbonded.itp │ │ ├── ffmissingdihedrals.itp │ │ ├── ffnonbonded.itp │ │ ├── forcefield.doc │ │ ├── forcefield.itp │ │ ├── ions.itp │ │ ├── lipid.c.tdb │ │ ├── lipid.hdb │ │ ├── lipid.n.tdb │ │ ├── lipid.r2b │ │ ├── lipid.rtp │ │ ├── metals.c.tdb │ │ ├── metals.hdb │ │ ├── metals.n.tdb │ │ ├── metals.r2b │ │ ├── metals.rtp │ │ ├── na.c.tdb │ │ ├── na.hdb │ │ ├── na.n.tdb │ │ ├── na.r2b │ │ ├── na.rtp │ │ ├── nbfix.itp │ │ ├── silicates.c.tdb │ │ ├── silicates.hdb │ │ ├── silicates.n.tdb │ │ ├── silicates.r2b │ │ ├── silicates.rtp │ │ ├── solvent.c.tdb │ │ ├── solvent.hdb │ │ ├── solvent.n.tdb │ │ ├── solvent.r2b │ │ ├── solvent.rtp │ │ ├── spc.itp │ │ ├── spce.itp │ │ ├── tip3p.itp │ │ ├── tip3p_original.itp │ │ ├── tip4p.itp │ │ ├── tip4pew.itp │ │ ├── tip5p.itp │ │ └── watermodels.dat │ ├── charmm36-mar2019-updated.ff │ │ ├── atomtypes.atp │ │ ├── cmap.itp │ │ ├── ffbonded.itp │ │ ├── ffbonded_UNDPP.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 │ │ └── watermodels.dat │ ├── charmm36-mar2019.ff │ │ ├── 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 │ │ └── watermodels.dat │ ├── charmm36_ljpme-jul2021.ff │ │ ├── aminoacids.arn │ │ ├── aminoacids.c.tdb │ │ ├── aminoacids.hdb │ │ ├── aminoacids.n.tdb │ │ ├── aminoacids.r2b │ │ ├── aminoacids.rtp │ │ ├── atomtypes.atp │ │ ├── carb.c.tdb │ │ ├── carb.hdb │ │ ├── carb.n.tdb │ │ ├── carb.r2b │ │ ├── carb.rtp │ │ ├── cgenff.c.tdb │ │ ├── cgenff.hdb │ │ ├── cgenff.n.tdb │ │ ├── cgenff.r2b │ │ ├── cgenff.rtp │ │ ├── cmap.itp │ │ ├── ethers.c.tdb │ │ ├── ethers.hdb │ │ ├── ethers.n.tdb │ │ ├── ethers.r2b │ │ ├── ethers.rtp │ │ ├── ffbonded.itp │ │ ├── ffmissingdihedrals.itp │ │ ├── ffnonbonded.itp │ │ ├── forcefield.doc │ │ ├── forcefield.itp │ │ ├── ions.itp │ │ ├── lipid.c.tdb │ │ ├── lipid.hdb │ │ ├── lipid.n.tdb │ │ ├── lipid.r2b │ │ ├── lipid.rtp │ │ ├── metals.c.tdb │ │ ├── metals.hdb │ │ ├── metals.n.tdb │ │ ├── metals.r2b │ │ ├── metals.rtp │ │ ├── na.c.tdb │ │ ├── na.hdb │ │ ├── na.n.tdb │ │ ├── na.r2b │ │ ├── na.rtp │ │ ├── nbfix.itp │ │ ├── silicates.c.tdb │ │ ├── silicates.hdb │ │ ├── silicates.n.tdb │ │ ├── silicates.r2b │ │ ├── silicates.rtp │ │ ├── solvent.c.tdb │ │ ├── solvent.hdb │ │ ├── solvent.n.tdb │ │ ├── solvent.r2b │ │ ├── solvent.rtp │ │ ├── spc.itp │ │ ├── spce.itp │ │ ├── tip3p.itp │ │ ├── tip3p_original.itp │ │ ├── tip4p.itp │ │ ├── tip4pew.itp │ │ ├── tip5p.itp │ │ └── watermodels.dat │ ├── charmm36_ljpme-jul2022.ff │ │ ├── aminoacids.arn │ │ ├── aminoacids.c.tdb │ │ ├── aminoacids.hdb │ │ ├── aminoacids.n.tdb │ │ ├── aminoacids.r2b │ │ ├── aminoacids.rtp │ │ ├── atomtypes.atp │ │ ├── carb.c.tdb │ │ ├── carb.hdb │ │ ├── carb.n.tdb │ │ ├── carb.r2b │ │ ├── carb.rtp │ │ ├── cgenff.c.tdb │ │ ├── cgenff.hdb │ │ ├── cgenff.n.tdb │ │ ├── cgenff.r2b │ │ ├── cgenff.rtp │ │ ├── cmap.itp │ │ ├── ethers.c.tdb │ │ ├── ethers.hdb │ │ ├── ethers.n.tdb │ │ ├── ethers.r2b │ │ ├── ethers.rtp │ │ ├── ffbonded.itp │ │ ├── ffmissingdihedrals.itp │ │ ├── ffnonbonded.itp │ │ ├── forcefield.doc │ │ ├── forcefield.itp │ │ ├── ions.itp │ │ ├── lipid.c.tdb │ │ ├── lipid.hdb │ │ ├── lipid.n.tdb │ │ ├── lipid.r2b │ │ ├── lipid.rtp │ │ ├── metals.c.tdb │ │ ├── metals.hdb │ │ ├── metals.n.tdb │ │ ├── metals.r2b │ │ ├── metals.rtp │ │ ├── na.c.tdb │ │ ├── na.hdb │ │ ├── na.n.tdb │ │ ├── na.r2b │ │ ├── na.rtp │ │ ├── nbfix.itp │ │ ├── silicates.c.tdb │ │ ├── silicates.hdb │ │ ├── silicates.n.tdb │ │ ├── silicates.r2b │ │ ├── silicates.rtp │ │ ├── solvent.c.tdb │ │ ├── solvent.hdb │ │ ├── solvent.n.tdb │ │ ├── solvent.r2b │ │ ├── solvent.rtp │ │ ├── spc.itp │ │ ├── spce.itp │ │ ├── tip3p.itp │ │ ├── tip3p_original.itp │ │ ├── tip4p.itp │ │ ├── tip4pew.itp │ │ ├── tip5p.itp │ │ └── watermodels.dat │ ├── oplsaa.ff │ │ ├── 1propanol.itp │ │ ├── aminoacids.c.tdb │ │ ├── aminoacids.hdb │ │ ├── aminoacids.n.tdb │ │ ├── aminoacids.r2b │ │ ├── aminoacids.rtp │ │ ├── aminoacids.vsd │ │ ├── atomname2type.n2t │ │ ├── atomtypes.atp │ │ ├── ethanol.itp │ │ ├── ffbonded.itp │ │ ├── ffnonbonded.itp │ │ ├── forcefield.doc │ │ ├── forcefield.itp │ │ ├── gbsa.itp │ │ ├── ions.itp │ │ ├── methanol.itp │ │ ├── spc.itp │ │ ├── spce.itp │ │ ├── tip3p.itp │ │ ├── tip4p.itp │ │ ├── tip4pew.itp │ │ ├── tip5p.itp │ │ ├── tip5pe.itp │ │ └── watermodels.dat │ ├── residuetypes.dat │ ├── specbond.dat │ └── test_charmm36-mar2019-updated.ff │ │ ├── atomtypes.atp │ │ ├── cmap.itp │ │ ├── ffbonded.itp │ │ ├── ffbonded_UNDPP.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 │ │ └── watermodels.dat └── fragments │ ├── SIRAH_charmm36 │ └── other │ │ ├── DAX │ │ ├── DAX.pdb │ │ └── DAX.top │ │ ├── DCX │ │ ├── DCX.pdb │ │ └── DCX.top │ │ ├── DGX │ │ ├── DGX.pdb │ │ └── DGX.top │ │ └── DTX │ │ ├── DTX.pdb │ │ └── DTX.top │ ├── martini_2-0_charmm36 │ ├── ions │ │ ├── CL │ │ │ ├── CL.itp │ │ │ ├── CL.pdb │ │ │ └── CL.top │ │ ├── K │ │ │ ├── K.itp │ │ │ ├── K.pdb │ │ │ └── K.top │ │ └── NA │ │ │ ├── NA.itp │ │ │ ├── NA.pdb │ │ │ └── NA.top │ ├── non_protein │ │ ├── ATP │ │ │ ├── ATP.itp │ │ │ ├── ATP.pdb │ │ │ ├── ATP.top │ │ │ └── ATP_posre.itp │ │ ├── CARD │ │ │ ├── CARD.itp │ │ │ ├── CARD.pdb │ │ │ └── CARD_posre.itp │ │ ├── CHOL │ │ │ ├── CHOL.itp │ │ │ ├── CHOL.pdb │ │ │ ├── CHOL.top │ │ │ └── CHOL_posre.itp │ │ ├── DPPC │ │ │ ├── DPPC.itp │ │ │ ├── DPPC.pdb │ │ │ └── DPPC_posre.itp │ │ ├── PIP2 │ │ │ ├── PIP2.itp │ │ │ ├── PIP2.pdb │ │ │ ├── PIP2.top │ │ │ └── PIP2_posre.itp │ │ ├── POPC │ │ │ ├── POPC.itp │ │ │ ├── POPC.pdb │ │ │ └── POPC_posre.itp │ │ ├── POPE │ │ │ ├── POPE.itp │ │ │ ├── POPE.pdb │ │ │ └── POPE_posre.itp │ │ ├── POPG │ │ │ ├── POPG.itp │ │ │ ├── POPG.pdb │ │ │ └── POPG_posre.itp │ │ └── UDP2 │ │ │ ├── UDP2.itp │ │ │ ├── UDP2.pdb │ │ │ └── UDP2_posre.itp │ ├── protein │ │ ├── ALA │ │ │ ├── ALA.pdb │ │ │ └── ALA.top │ │ ├── ARG │ │ │ ├── ARG.pdb │ │ │ └── ARG.top │ │ ├── ASN │ │ │ ├── ASN.pdb │ │ │ └── ASN.top │ │ ├── ASP │ │ │ ├── ASP.pdb │ │ │ └── ASP.top │ │ ├── CYS │ │ │ ├── CYS.pdb │ │ │ └── CYS.top │ │ ├── GLN │ │ │ ├── GLN.pdb │ │ │ └── GLN.top │ │ ├── GLU │ │ │ ├── GLU.pdb │ │ │ └── GLU.top │ │ ├── GLY │ │ │ ├── GLY.pdb │ │ │ └── GLY.top │ │ ├── HIS │ │ │ ├── HIS.pdb │ │ │ └── HIS.top │ │ ├── ILE │ │ │ ├── ILE.pdb │ │ │ └── ILE.top │ │ ├── LEU │ │ │ ├── LEU.pdb │ │ │ └── LEU.top │ │ ├── LYS │ │ │ ├── LYS.pdb │ │ │ └── LYS.top │ │ ├── MET │ │ │ ├── MET.pdb │ │ │ └── MET.top │ │ ├── PHE │ │ │ ├── PHE.pdb │ │ │ └── PHE.top │ │ ├── PRO │ │ │ ├── PRO.pdb │ │ │ └── PRO.top │ │ ├── SER │ │ │ ├── SER.pdb │ │ │ └── SER.top │ │ ├── THR │ │ │ ├── THR.pdb │ │ │ └── THR.top │ │ ├── TRP │ │ │ ├── TRP.pdb │ │ │ └── TRP.top │ │ ├── TYR │ │ │ ├── TYR.pdb │ │ │ └── TYR.top │ │ └── VAL │ │ │ ├── VAL.pdb │ │ │ └── VAL.top │ ├── protein_modified │ │ ├── CYSD │ │ │ ├── CYSD.pdb │ │ │ └── CYSD.top │ │ ├── CYST │ │ │ ├── CYST.pdb │ │ │ └── CYST.top │ │ └── _SERP │ │ │ └── ser.pdb │ └── solvent │ │ └── W │ │ ├── SPC.itp │ │ ├── SPC.pdb │ │ ├── SPC.top │ │ ├── SPCE.itp │ │ ├── SPCE.pdb │ │ ├── SPCE.top │ │ ├── TIP3P.itp │ │ ├── TIP3P.pdb │ │ ├── TIP3P.top │ │ ├── TIP4P.itp │ │ ├── TIP4P.pdb │ │ └── TIP4P.top │ ├── martini_2-2_charmm36-VS │ ├── ions │ │ ├── CL │ │ │ ├── CL.itp │ │ │ ├── CL.pdb │ │ │ └── CL.top │ │ ├── K │ │ │ ├── K.itp │ │ │ ├── K.pdb │ │ │ └── K.top │ │ └── NA │ │ │ ├── NA.itp │ │ │ ├── NA.pdb │ │ │ └── NA.top │ ├── non_protein │ │ ├── ATP │ │ │ ├── ATP.itp │ │ │ ├── ATP.pdb │ │ │ ├── ATP.top │ │ │ └── ATP_posre.itp │ │ ├── CHOL │ │ │ ├── CHOL.itp │ │ │ ├── CHOL.pdb │ │ │ ├── CHOL.top │ │ │ └── CHOL_posre.itp │ │ ├── PIP2 │ │ │ ├── PIP2.itp │ │ │ ├── PIP2.pdb │ │ │ ├── PIP2.top │ │ │ └── PIP2_posre.itp │ │ ├── POPA │ │ │ ├── POPA.itp │ │ │ ├── POPA.pdb │ │ │ └── POPA_posre.itp │ │ ├── POPC │ │ │ ├── POPC.itp │ │ │ ├── POPC.pdb │ │ │ └── POPC_posre.itp │ │ ├── POPE │ │ │ ├── POPE.itp │ │ │ ├── POPE.pdb │ │ │ └── POPE_posre.itp │ │ ├── POPG │ │ │ ├── POPG.itp │ │ │ ├── POPG.pdb │ │ │ └── POPG_posre.itp │ │ └── UDP2 │ │ │ ├── UDP2.itp │ │ │ ├── UDP2.pdb │ │ │ └── UDP2_posre.itp │ ├── protein │ │ ├── ALA │ │ │ ├── ALA.pdb │ │ │ └── ALA.top │ │ ├── ARG │ │ │ ├── ARG.pdb │ │ │ └── ARG.top │ │ ├── ASN │ │ │ ├── ASN.pdb │ │ │ └── ASN.top │ │ ├── ASP │ │ │ ├── ASP.pdb │ │ │ └── ASP.top │ │ ├── CYS │ │ │ ├── CYS.pdb │ │ │ └── CYS.top │ │ ├── GLN │ │ │ ├── GLN.pdb │ │ │ └── GLN.top │ │ ├── GLU │ │ │ ├── GLU.pdb │ │ │ └── GLU.top │ │ ├── GLY │ │ │ ├── GLY.pdb │ │ │ └── GLY.top │ │ ├── HIS │ │ │ ├── HIS.pdb │ │ │ └── HIS.top │ │ ├── ILE │ │ │ ├── ILE.pdb │ │ │ └── ILE.top │ │ ├── LEU │ │ │ ├── LEU.pdb │ │ │ └── LEU.top │ │ ├── LYS │ │ │ ├── LYS.pdb │ │ │ └── LYS.top │ │ ├── MET │ │ │ ├── MET.pdb │ │ │ └── MET.top │ │ ├── PHE │ │ │ ├── PHE.pdb │ │ │ └── PHE.top │ │ ├── PRO │ │ │ ├── PRO.pdb │ │ │ └── PRO.top │ │ ├── SER │ │ │ ├── SER.pdb │ │ │ └── SER.top │ │ ├── THR │ │ │ ├── THR.pdb │ │ │ └── THR.top │ │ ├── TRP │ │ │ ├── TRP.pdb │ │ │ └── TRP.top │ │ ├── TYR │ │ │ ├── TYR.pdb │ │ │ └── TYR.top │ │ ├── VAL │ │ │ ├── VAL.pdb │ │ │ └── VAL.top │ │ ├── _ACE │ │ │ └── ACE.pdb │ │ └── _NME │ │ │ └── NME.pdb │ ├── protein_modified │ │ ├── CYSD │ │ │ ├── CYSD.pdb │ │ │ └── CYSD.top │ │ ├── CYST │ │ │ ├── CYST.pdb │ │ │ └── CYST.top │ │ ├── GLYM │ │ │ ├── GLYM.pdb │ │ │ └── GLYM.top │ │ ├── GLYP │ │ │ ├── GLYP.pdb │ │ │ └── GLYP.top │ │ └── _SERP │ │ │ └── ser.pdb │ └── solvent │ │ └── W │ │ ├── SPC.itp │ │ ├── SPC.pdb │ │ ├── SPC.top │ │ ├── SPCE.itp │ │ ├── SPCE.pdb │ │ ├── SPCE.top │ │ ├── TIP3P.itp │ │ ├── TIP3P.pdb │ │ ├── TIP3P.top │ │ ├── TIP4P.itp │ │ ├── TIP4P.pdb │ │ └── TIP4P.top │ ├── martini_2-2_charmm36 │ ├── ions │ │ ├── CL │ │ │ ├── CL.itp │ │ │ ├── CL.pdb │ │ │ └── CL.top │ │ ├── K │ │ │ ├── K.itp │ │ │ ├── K.pdb │ │ │ └── K.top │ │ └── NA │ │ │ ├── NA.itp │ │ │ ├── NA.pdb │ │ │ └── NA.top │ ├── non_protein │ │ ├── 4HPA │ │ │ ├── 4HPA.itp │ │ │ ├── 4HPA.pdb │ │ │ ├── 4HPA.top │ │ │ └── 4HPA_posre.itp │ │ ├── ATP │ │ │ ├── ATP.itp │ │ │ ├── ATP.pdb │ │ │ └── ATP_posre.itp │ │ ├── BACI │ │ │ ├── BACI.itp │ │ │ ├── BACI.pdb │ │ │ ├── BACI.top │ │ │ └── BACI_posre.itp │ │ ├── CARD │ │ │ ├── CARD.itp │ │ │ ├── CARD.pdb │ │ │ └── CARD_posre.itp │ │ ├── CDL2 │ │ │ ├── CDL2.itp │ │ │ ├── CDL2.pdb │ │ │ └── CDL2_posre.itp │ │ ├── CHOL │ │ │ ├── CHOL.itp │ │ │ ├── CHOL.pdb │ │ │ ├── CHOL.top │ │ │ └── CHOL_posre.itp │ │ ├── DGPA │ │ │ ├── DGPA.itp │ │ │ ├── DGPA.pdb │ │ │ └── DGPA_posre.itp │ │ ├── DGPC │ │ │ ├── DGPC.itp │ │ │ ├── DGPC.pdb │ │ │ └── DGPC_posre.itp │ │ ├── DGPE │ │ │ ├── DGPE.itp │ │ │ ├── DGPE.pdb │ │ │ ├── DGPE.pdb2 │ │ │ └── DGPE_posre.itp │ │ ├── DGPS │ │ │ ├── DGPS.itp │ │ │ ├── DGPS.pdb │ │ │ └── DGPS_posre.itp │ │ ├── DLPA │ │ │ ├── DLPA.itp │ │ │ ├── DLPA.pdb │ │ │ └── DLPA_posre.itp │ │ ├── DLPC │ │ │ ├── DLPC.itp │ │ │ ├── DLPC.pdb │ │ │ └── DLPC_posre.itp │ │ ├── DLPE │ │ │ ├── DLPE.itp │ │ │ ├── DLPE.pdb │ │ │ └── DLPE_posre.itp │ │ ├── DLPG │ │ │ ├── DLPG.itp │ │ │ ├── DLPG.pdb │ │ │ └── DLPG_posre.itp │ │ ├── DLPS │ │ │ ├── DLPS.itp │ │ │ ├── DLPS.pdb │ │ │ └── DLPS_posre.itp │ │ ├── DMPC │ │ │ ├── DMPC.itp │ │ │ ├── DMPC.pdb │ │ │ └── DMPC_posre.itp │ │ ├── DMPE │ │ │ ├── DMPE.itp │ │ │ ├── DMPE.pdb │ │ │ └── DMPE_posre.itp │ │ ├── DMPI │ │ │ ├── DMPI.itp │ │ │ ├── DMPI.pdb │ │ │ └── DMPI_posre.itp │ │ ├── DMPS │ │ │ ├── DMPS.itp │ │ │ ├── DMPS.pdb │ │ │ └── DMPS_posre.itp │ │ ├── DNPA │ │ │ ├── DNPA.itp │ │ │ ├── DNPA.pdb │ │ │ └── DNPA_posre.itp │ │ ├── DNPC │ │ │ ├── DNPC.itp │ │ │ ├── DNPC.pdb │ │ │ └── DNPC_posre.itp │ │ ├── DNPE │ │ │ ├── DNPE.itp │ │ │ ├── DNPE.pdb │ │ │ └── DNPE_posre.itp │ │ ├── DNPG │ │ │ ├── DNPG.itp │ │ │ ├── DNPG.pdb │ │ │ └── DNPG_posre.itp │ │ ├── DNPS │ │ │ ├── DNPS.itp │ │ │ ├── DNPS.pdb │ │ │ └── DNPS_posre.itp │ │ ├── DOPA │ │ │ ├── DOPA.itp │ │ │ ├── DOPA.pdb │ │ │ └── DOPA_posre.itp │ │ ├── DOPC │ │ │ ├── DOPC.itp │ │ │ ├── DOPC.pdb │ │ │ └── DOPC_posre.itp │ │ ├── DOPE │ │ │ ├── DOPE.itp │ │ │ ├── DOPE.pdb │ │ │ └── DOPE_posre.itp │ │ ├── DOPG │ │ │ ├── DOPG.itp │ │ │ ├── DOPG.pdb │ │ │ └── DOPG_posre.itp │ │ ├── DOPS │ │ │ ├── DOPS.itp │ │ │ ├── DOPS.pdb │ │ │ └── DOPS_posre.itp │ │ ├── DPG1 │ │ │ ├── .DS_Store │ │ │ ├── DPG1.itp │ │ │ ├── DPG1.pdb │ │ │ └── DPG1_posre.itp │ │ ├── DPG3 │ │ │ ├── DPG3.itp │ │ │ ├── DPG3.pdb │ │ │ └── DPG3_posre.itp │ │ ├── DPPA │ │ │ ├── DPPA.itp │ │ │ ├── DPPA.pdb │ │ │ └── DPPA_posre.itp │ │ ├── DPPC │ │ │ ├── DPPC.itp │ │ │ ├── DPPC.pdb │ │ │ └── DPPC_posre.itp │ │ ├── DPPE │ │ │ ├── DPPE.itp │ │ │ ├── DPPE.pdb │ │ │ └── DPPE_posre.itp │ │ ├── DPPG │ │ │ ├── DPPG.itp │ │ │ ├── DPPG.pdb │ │ │ └── DPPG_posre.itp │ │ ├── DPPS │ │ │ ├── DPPS.itp │ │ │ ├── DPPS.pdb │ │ │ └── DPPS_posre.itp │ │ ├── DYPA │ │ │ ├── DYPA.itp │ │ │ ├── DYPA.pdb │ │ │ └── DYPA_posre.itp │ │ ├── DYPC │ │ │ ├── DYPC.itp │ │ │ ├── DYPC.pdb │ │ │ └── DYPC_posre.itp │ │ ├── DYPE │ │ │ ├── DYPE.itp │ │ │ ├── DYPE.pdb │ │ │ └── DYPE_posre.itp │ │ ├── DYPG │ │ │ ├── DYPG.itp │ │ │ ├── DYPG.pdb │ │ │ └── DYPG_posre.itp │ │ ├── DYPS │ │ │ ├── DYPS.itp │ │ │ ├── DYPS.pdb │ │ │ └── DYPS_posre.itp │ │ ├── ERGO │ │ │ ├── ERGO.itp │ │ │ ├── ERGO.pdb │ │ │ ├── ERGO.top │ │ │ └── ERGO_posre.itp │ │ ├── FEN │ │ │ ├── FEN.itp │ │ │ ├── FEN.pdb │ │ │ └── FEN_posre.itp │ │ ├── HPPA │ │ │ ├── HPPA.itp │ │ │ ├── HPPA.pdb │ │ │ ├── HPPA.top │ │ │ └── HPPA_posre.itp │ │ ├── LI10 │ │ │ ├── LI10.itp │ │ │ ├── LI10.pdb │ │ │ ├── LI10_posres.itp │ │ │ └── LIP10.top │ │ ├── LI12 │ │ │ ├── LI12.itp │ │ │ ├── LI12.pdb │ │ │ ├── LI12_posres.itp │ │ │ └── LIP12.top │ │ ├── LIP1 │ │ │ ├── LIP1.itp │ │ │ ├── LIP1.pdb │ │ │ ├── LIP1_posre.itp │ │ │ └── LIP2.top │ │ ├── LIP2 │ │ │ ├── LIP2.itp │ │ │ ├── LIP2.pdb │ │ │ ├── LIP2.top │ │ │ ├── LIP2 │ │ │ │ ├── LIP2.itp │ │ │ │ ├── LIP2.pdb │ │ │ │ └── LIP2_posres.itp │ │ │ ├── LIP2_posres.itp │ │ │ └── __MACOSX │ │ │ │ └── LIP2 │ │ │ │ ├── ._LIP2.itp │ │ │ │ ├── ._LIP2.pdb │ │ │ │ └── ._LIP2_posres.itp │ │ ├── LIP4 │ │ │ ├── LIP4.itp │ │ │ ├── LIP4.pdb │ │ │ ├── LIP4.top │ │ │ └── LIP4_posres.itp │ │ ├── LIP6 │ │ │ ├── LIP6.itp │ │ │ ├── LIP6.pdb │ │ │ ├── LIP6.top │ │ │ └── LIP6_posres.itp │ │ ├── LIP8 │ │ │ ├── LIP8.itp │ │ │ ├── LIP8.pdb │ │ │ ├── LIP8.top │ │ │ └── LIP8_posres.itp │ │ ├── LIPA │ │ │ ├── LIPA.itp │ │ │ ├── LIPA.pdb │ │ │ └── LIPA_posre.itp │ │ ├── OANT │ │ │ ├── OANT.itp │ │ │ ├── OANT.pdb │ │ │ ├── OANT_posre.itp │ │ │ └── _OANT.top │ │ ├── PCRE │ │ │ ├── PCRE.itp │ │ │ ├── PCRE.pdb │ │ │ ├── PCRE.top │ │ │ └── PCRE_posre.itp │ │ ├── PIP2 │ │ │ ├── PIP2.itp │ │ │ ├── PIP2.pdb │ │ │ └── PIP2_posre.itp │ │ ├── PIP3 │ │ │ ├── PIP3.itp │ │ │ ├── PIP3.pdb │ │ │ ├── PIP3.pdb2 │ │ │ └── PIP3_posre.itp │ │ ├── POP2 │ │ │ ├── POP2.itp │ │ │ ├── POP2.pdb │ │ │ └── POP2_posre.itp │ │ ├── POPA │ │ │ ├── POPA.itp │ │ │ ├── POPA.pdb │ │ │ └── POPA_posre.itp │ │ ├── POPC │ │ │ ├── POPC.itp │ │ │ ├── POPC.pdb │ │ │ └── POPC_posre.itp │ │ ├── POPE │ │ │ ├── POPE.itp │ │ │ ├── POPE.pdb │ │ │ └── POPE_posre.itp │ │ ├── POPG │ │ │ ├── POPG.itp │ │ │ ├── POPG.pdb │ │ │ └── POPG_posre.itp │ │ ├── POPI │ │ │ ├── POPI.itp │ │ │ ├── POPI.pdb │ │ │ ├── POPI.pdb2 │ │ │ └── POPI_posre.itp │ │ ├── POPI1_3 │ │ │ ├── POPI1_3.itp │ │ │ ├── POPI1_3.pdb │ │ │ └── POPI1_3_posre.itp │ │ ├── POPI1_4 │ │ │ ├── POPI1_4.itp │ │ │ ├── POPI1_4.pdb │ │ │ └── POPI1_4_posre.itp │ │ ├── POPI1_5 │ │ │ ├── POPI1_5.itp │ │ │ ├── POPI1_5.pdb │ │ │ └── POPI1_5_posre.itp │ │ ├── POPI2_3-4_3 │ │ │ ├── POPI2_3-4_3.itp │ │ │ ├── POPI2_3-4_3.pdb │ │ │ └── POPI2_3-4_3_posre.itp │ │ ├── POPI2_3-4_4 │ │ │ ├── POPI2_3-4_4.itp │ │ │ ├── POPI2_3-4_4.pdb │ │ │ └── POPI2_3-4_4_posre.itp │ │ ├── POPI2_3-5 │ │ │ ├── POPI2_3-5.itp │ │ │ ├── POPI2_3-5.pdb │ │ │ ├── POPI2_3-5.pdb2 │ │ │ └── POPI2_3-5_posre.itp │ │ ├── POPI2_3-5_3 │ │ │ ├── POPI2_3-5_3.itp │ │ │ ├── POPI2_3-5_3.pdb │ │ │ └── POPI2_3-5_3_posre.itp │ │ ├── POPI2_3-5_5 │ │ │ ├── POPI2_3-5_5.itp │ │ │ ├── POPI2_3-5_5.pdb │ │ │ └── POPI2_3-5_5_posre.itp │ │ ├── POPI2_4-5_4 │ │ │ ├── POPI2_4-5_4.itp │ │ │ ├── POPI2_4-5_4.pdb │ │ │ ├── POPI2_4-5_4.pdb2 │ │ │ └── POPI2_4-5_4_posre.itp │ │ ├── POPI2_4-5_5 │ │ │ ├── POPI2_4-5_5.itp │ │ │ ├── POPI2_4-5_5.pdb │ │ │ ├── POPI2_4-5_5.pdb2 │ │ │ └── POPI2_4-5_5_posre.itp │ │ ├── POPI3_3-4-5 │ │ │ ├── POPI3_3-4-5.itp │ │ │ ├── POPI3_3-4-5.pdb │ │ │ └── POPI3_3-4-5_posre.itp │ │ ├── POPI3_3-4-5_3 │ │ │ ├── POPI3_3-4-5_3.itp │ │ │ ├── POPI3_3-4-5_3.pdb │ │ │ └── POPI3_3-4-5_3_posre.itp │ │ ├── POPI3_3-4-5_4 │ │ │ ├── POPI3_3-4-5_4.itp │ │ │ ├── POPI3_3-4-5_4.pdb │ │ │ └── POPI3_3-4-5_4_posre.itp │ │ ├── POPI3_3-4-5_5 │ │ │ ├── POPI3_3-4-5_5.itp │ │ │ ├── POPI3_3-4-5_5.pdb │ │ │ └── POPI3_3-4-5_5_posre.itp │ │ ├── POPS │ │ │ ├── POPS.itp │ │ │ ├── POPS.pdb │ │ │ ├── POPS.pdb2 │ │ │ └── POPS_posre.itp │ │ ├── RAMP │ │ │ ├── RAMP.itp │ │ │ ├── RAMP.pdb │ │ │ └── RAMP_posre.itp │ │ ├── REMP │ │ │ ├── REMP.itp │ │ │ ├── REMP.pdb │ │ │ └── REMP_posre.itp │ │ ├── UDP1 │ │ │ ├── UDP1.itp │ │ │ ├── UDP1.pdb │ │ │ └── UDP1_posre.itp │ │ └── UDP2 │ │ │ ├── UDP2.itp │ │ │ ├── UDP2.pdb │ │ │ └── UDP2_posre.itp │ ├── other │ │ ├── DA │ │ │ ├── DA.pdb │ │ │ └── DA.top │ │ ├── DC │ │ │ ├── DC.pdb │ │ │ └── DC.top │ │ ├── DG │ │ │ ├── DG.pdb │ │ │ └── DG.top │ │ ├── DT │ │ │ ├── DT.pdb │ │ │ └── DT.top │ │ ├── _NAG │ │ │ ├── #NAG.pdb.1# │ │ │ ├── NAG.pdb │ │ │ └── NAG.top │ │ ├── _NAM │ │ │ ├── #NAM.pdb.1# │ │ │ ├── #NAM.pdb.2# │ │ │ ├── #NAML.pdb.1# │ │ │ ├── NAM.pdb │ │ │ └── NAML.pdb │ │ ├── _PEPL │ │ │ ├── PEPL.pdb │ │ │ └── PEPL.top │ │ ├── _PEPS │ │ │ ├── PEPS.pdb │ │ │ └── PEPS.top │ │ └── _UDP2 │ │ │ └── UDP2.pdb │ ├── protein │ │ ├── ALA │ │ │ ├── ALA.pdb │ │ │ └── ALA.top │ │ ├── ARG │ │ │ ├── ARG.pdb │ │ │ └── ARG.top │ │ ├── ASN │ │ │ ├── ASN.pdb │ │ │ └── ASN.top │ │ ├── ASP │ │ │ ├── ASP.pdb │ │ │ └── ASP.top │ │ ├── CYS │ │ │ ├── CYS.pdb │ │ │ └── CYS.top │ │ ├── GLN │ │ │ ├── GLN.pdb │ │ │ └── GLN.top │ │ ├── GLU │ │ │ ├── GLU.pdb │ │ │ └── GLU.top │ │ ├── GLY │ │ │ ├── GLY.pdb │ │ │ └── GLY.top │ │ ├── HIS │ │ │ ├── HIS.pdb │ │ │ └── HIS.top │ │ ├── ILE │ │ │ ├── ILE.pdb │ │ │ └── ILE.top │ │ ├── LEU │ │ │ ├── LEU.pdb │ │ │ └── LEU.top │ │ ├── LYS │ │ │ ├── LYS.pdb │ │ │ └── LYS.top │ │ ├── MET │ │ │ ├── MET.pdb │ │ │ └── MET.top │ │ ├── PHE │ │ │ ├── PHE.pdb │ │ │ └── PHE.top │ │ ├── PRO │ │ │ ├── PRO.pdb │ │ │ └── PRO.top │ │ ├── SER │ │ │ ├── SER.pdb │ │ │ └── SER.top │ │ ├── THR │ │ │ ├── THR.pdb │ │ │ └── THR.top │ │ ├── TRP │ │ │ ├── TRP.pdb │ │ │ └── TRP.top │ │ ├── TYR │ │ │ ├── TYR.pdb │ │ │ └── TYR.top │ │ └── VAL │ │ │ ├── VAL.pdb │ │ │ └── VAL.top │ ├── protein_modified │ │ ├── CYSD │ │ │ ├── CYSD.pdb │ │ │ └── CYSD.top │ │ ├── CYST │ │ │ ├── CYST.pdb │ │ │ └── CYST.top │ │ ├── GLYM │ │ │ ├── GLYM.pdb │ │ │ └── GLYM.top │ │ ├── GLYP │ │ │ ├── GLYP.pdb │ │ │ └── GLYP.top │ │ ├── _LYSM │ │ │ ├── #conf.gro.1# │ │ │ ├── #posre.itp.1# │ │ │ ├── #topol.top.1# │ │ │ ├── LYSM.pdb │ │ │ ├── conf.gro │ │ │ ├── mdout.mdp │ │ │ ├── posre.itp │ │ │ ├── step5_input.pdb │ │ │ ├── topol.edr │ │ │ ├── topol.gro │ │ │ ├── topol.log │ │ │ ├── topol.top │ │ │ ├── topol.tpr │ │ │ └── topol.trr │ │ ├── _SERP │ │ │ └── ser.pdb │ │ └── _others │ │ │ ├── LYS.pdb │ │ │ ├── cys.pdb │ │ │ ├── gly.pdb │ │ │ └── lys.pdb │ └── solvent │ │ └── W │ │ ├── SPC.itp │ │ ├── SPC.pdb │ │ ├── SPC.top │ │ ├── SPCE.itp │ │ ├── SPCE.pdb │ │ ├── SPCE.top │ │ ├── TIP3P.itp │ │ ├── TIP3P.pdb │ │ ├── TIP3P.top │ │ ├── TIP4P.itp │ │ ├── TIP4P.pdb │ │ └── TIP4P.top │ ├── martini_2-2_charmm36_Jul2021 │ ├── ions │ │ ├── CL │ │ │ ├── CL.itp │ │ │ ├── CL.pdb │ │ │ └── CL.top │ │ ├── K │ │ │ ├── K.itp │ │ │ ├── K.pdb │ │ │ └── K.top │ │ └── NA │ │ │ ├── NA.itp │ │ │ ├── NA.pdb │ │ │ └── NA.top │ ├── non_protein │ │ ├── 4HPA │ │ │ ├── 4HPA.itp │ │ │ ├── 4HPA.pdb │ │ │ ├── 4HPA.top │ │ │ └── 4HPA_posre.itp │ │ ├── ATP │ │ │ ├── ATP.itp │ │ │ ├── ATP.pdb │ │ │ └── ATP_posre.itp │ │ ├── BACI │ │ │ ├── BACI.itp │ │ │ ├── BACI.pdb │ │ │ ├── BACI.top │ │ │ └── BACI_posre.itp │ │ ├── CARD │ │ │ ├── CARD.itp │ │ │ ├── CARD.pdb │ │ │ └── CARD_posre.itp │ │ ├── CDL2 │ │ │ ├── CDL2.itp │ │ │ ├── CDL2.pdb │ │ │ └── CDL2_posre.itp │ │ ├── CHOL │ │ │ ├── CHOL.itp │ │ │ ├── CHOL.pdb │ │ │ ├── CHOL.top │ │ │ └── CHOL_posre.itp │ │ ├── DGPA │ │ │ ├── DGPA.itp │ │ │ ├── DGPA.pdb │ │ │ └── DGPA_posre.itp │ │ ├── DGPC │ │ │ ├── DGPC.itp │ │ │ ├── DGPC.pdb │ │ │ └── DGPC_posre.itp │ │ ├── DGPE │ │ │ ├── DGPE.itp │ │ │ ├── DGPE.pdb │ │ │ ├── DGPE.pdb2 │ │ │ └── DGPE_posre.itp │ │ ├── DGPS │ │ │ ├── DGPS.itp │ │ │ ├── DGPS.pdb │ │ │ └── DGPS_posre.itp │ │ ├── DLPA │ │ │ ├── DLPA.itp │ │ │ ├── DLPA.pdb │ │ │ └── DLPA_posre.itp │ │ ├── DLPC │ │ │ ├── DLPC.itp │ │ │ ├── DLPC.pdb │ │ │ └── DLPC_posre.itp │ │ ├── DLPE │ │ │ ├── DLPE.itp │ │ │ ├── DLPE.pdb │ │ │ └── DLPE_posre.itp │ │ ├── DLPG │ │ │ ├── DLPG.itp │ │ │ ├── DLPG.pdb │ │ │ └── DLPG_posre.itp │ │ ├── DLPS │ │ │ ├── DLPS.itp │ │ │ ├── DLPS.pdb │ │ │ └── DLPS_posre.itp │ │ ├── DMPC │ │ │ ├── DMPC.itp │ │ │ ├── DMPC.pdb │ │ │ └── DMPC_posre.itp │ │ ├── DMPE │ │ │ ├── DMPE.itp │ │ │ ├── DMPE.pdb │ │ │ └── DMPE_posre.itp │ │ ├── DMPI │ │ │ ├── DMPI.itp │ │ │ ├── DMPI.pdb │ │ │ └── DMPI_posre.itp │ │ ├── DMPS │ │ │ ├── DMPS.itp │ │ │ ├── DMPS.pdb │ │ │ └── DMPS_posre.itp │ │ ├── DNPA │ │ │ ├── DNPA.itp │ │ │ ├── DNPA.pdb │ │ │ └── DNPA_posre.itp │ │ ├── DNPC │ │ │ ├── DNPC.itp │ │ │ ├── DNPC.pdb │ │ │ └── DNPC_posre.itp │ │ ├── DNPE │ │ │ ├── DNPE.itp │ │ │ ├── DNPE.pdb │ │ │ └── DNPE_posre.itp │ │ ├── DNPG │ │ │ ├── DNPG.itp │ │ │ ├── DNPG.pdb │ │ │ └── DNPG_posre.itp │ │ ├── DNPS │ │ │ ├── DNPS.itp │ │ │ ├── DNPS.pdb │ │ │ └── DNPS_posre.itp │ │ ├── DOPA │ │ │ ├── DOPA.itp │ │ │ ├── DOPA.pdb │ │ │ └── DOPA_posre.itp │ │ ├── DOPC │ │ │ ├── DOPC.itp │ │ │ ├── DOPC.pdb │ │ │ └── DOPC_posre.itp │ │ ├── DOPE │ │ │ ├── DOPE.itp │ │ │ ├── DOPE.pdb │ │ │ └── DOPE_posre.itp │ │ ├── DOPG │ │ │ ├── DOPG.itp │ │ │ ├── DOPG.pdb │ │ │ └── DOPG_posre.itp │ │ ├── DOPS │ │ │ ├── DOPS.itp │ │ │ ├── DOPS.pdb │ │ │ └── DOPS_posre.itp │ │ ├── DPG1 │ │ │ ├── .DS_Store │ │ │ ├── DPG1.itp │ │ │ ├── DPG1.pdb │ │ │ └── DPG1_posre.itp │ │ ├── DPG3 │ │ │ ├── DPG3.itp │ │ │ ├── DPG3.pdb │ │ │ └── DPG3_posre.itp │ │ ├── DPPA │ │ │ ├── DPPA.itp │ │ │ ├── DPPA.pdb │ │ │ └── DPPA_posre.itp │ │ ├── DPPC │ │ │ ├── DPPC.itp │ │ │ ├── DPPC.pdb │ │ │ └── DPPC_posre.itp │ │ ├── DPPE │ │ │ ├── DPPE.itp │ │ │ ├── DPPE.pdb │ │ │ └── DPPE_posre.itp │ │ ├── DPPG │ │ │ ├── DPPG.itp │ │ │ ├── DPPG.pdb │ │ │ └── DPPG_posre.itp │ │ ├── DPPS │ │ │ ├── DPPS.itp │ │ │ ├── DPPS.pdb │ │ │ └── DPPS_posre.itp │ │ ├── DYPA │ │ │ ├── DYPA.itp │ │ │ ├── DYPA.pdb │ │ │ └── DYPA_posre.itp │ │ ├── DYPC │ │ │ ├── DYPC.itp │ │ │ ├── DYPC.pdb │ │ │ └── DYPC_posre.itp │ │ ├── DYPE │ │ │ ├── DYPE.itp │ │ │ ├── DYPE.pdb │ │ │ └── DYPE_posre.itp │ │ ├── DYPG │ │ │ ├── DYPG.itp │ │ │ ├── DYPG.pdb │ │ │ └── DYPG_posre.itp │ │ ├── DYPS │ │ │ ├── DYPS.itp │ │ │ ├── DYPS.pdb │ │ │ └── DYPS_posre.itp │ │ ├── ERGO │ │ │ ├── ERGO.itp │ │ │ ├── ERGO.pdb │ │ │ ├── ERGO.top │ │ │ └── ERGO_posre.itp │ │ ├── FEN │ │ │ ├── FEN.itp │ │ │ ├── FEN.pdb │ │ │ └── FEN_posre.itp │ │ ├── HPPA │ │ │ ├── HPPA.itp │ │ │ ├── HPPA.pdb │ │ │ ├── HPPA.top │ │ │ └── HPPA_posre.itp │ │ ├── LI10 │ │ │ ├── LI10.itp │ │ │ ├── LI10.pdb │ │ │ ├── LI10_posres.itp │ │ │ └── LIP10.top │ │ ├── LI12 │ │ │ ├── LI12.itp │ │ │ ├── LI12.pdb │ │ │ ├── LI12_posres.itp │ │ │ └── LIP12.top │ │ ├── LIP1 │ │ │ ├── LIP1.itp │ │ │ ├── LIP1.pdb │ │ │ ├── LIP1_posre.itp │ │ │ └── LIP2.top │ │ ├── LIP2 │ │ │ ├── LIP2.itp │ │ │ ├── LIP2.pdb │ │ │ ├── LIP2.top │ │ │ ├── LIP2 │ │ │ │ ├── LIP2.itp │ │ │ │ ├── LIP2.pdb │ │ │ │ └── LIP2_posres.itp │ │ │ ├── LIP2_posres.itp │ │ │ └── __MACOSX │ │ │ │ └── LIP2 │ │ │ │ ├── ._LIP2.itp │ │ │ │ ├── ._LIP2.pdb │ │ │ │ └── ._LIP2_posres.itp │ │ ├── LIP4 │ │ │ ├── LIP4.itp │ │ │ ├── LIP4.pdb │ │ │ ├── LIP4.top │ │ │ └── LIP4_posres.itp │ │ ├── LIP6 │ │ │ ├── LIP6.itp │ │ │ ├── LIP6.pdb │ │ │ ├── LIP6.top │ │ │ └── LIP6_posres.itp │ │ ├── LIP8 │ │ │ ├── LIP8.itp │ │ │ ├── LIP8.pdb │ │ │ ├── LIP8.top │ │ │ └── LIP8_posres.itp │ │ ├── LIPA │ │ │ ├── LIPA.itp │ │ │ ├── LIPA.pdb │ │ │ └── LIPA_posre.itp │ │ ├── OANT │ │ │ ├── OANT.itp │ │ │ ├── OANT.pdb │ │ │ ├── OANT_posre.itp │ │ │ └── _OANT.top │ │ ├── PCRE │ │ │ ├── PCRE.itp │ │ │ ├── PCRE.pdb │ │ │ ├── PCRE.top │ │ │ └── PCRE_posre.itp │ │ ├── PIP2 │ │ │ ├── PIP2.itp │ │ │ ├── PIP2.pdb │ │ │ └── PIP2_posre.itp │ │ ├── PIP3 │ │ │ ├── PIP3.itp │ │ │ ├── PIP3.pdb │ │ │ ├── PIP3.pdb2 │ │ │ └── PIP3_posre.itp │ │ ├── POP2 │ │ │ ├── POP2.itp │ │ │ ├── POP2.pdb │ │ │ └── POP2_posre.itp │ │ ├── POPA │ │ │ ├── POPA.itp │ │ │ ├── POPA.pdb │ │ │ └── POPA_posre.itp │ │ ├── POPC │ │ │ ├── POPC.itp │ │ │ ├── POPC.pdb │ │ │ └── POPC_posre.itp │ │ ├── POPE │ │ │ ├── POPE.itp │ │ │ ├── POPE.pdb │ │ │ └── POPE_posre.itp │ │ ├── POPG │ │ │ ├── POPG.itp │ │ │ ├── POPG.pdb │ │ │ └── POPG_posre.itp │ │ ├── POPI │ │ │ ├── POPI.itp │ │ │ ├── POPI.pdb │ │ │ ├── POPI.pdb2 │ │ │ └── POPI_posre.itp │ │ ├── POPI1_3 │ │ │ ├── POPI1_3.itp │ │ │ ├── POPI1_3.pdb │ │ │ └── POPI1_3_posre.itp │ │ ├── POPI1_4 │ │ │ ├── POPI1_4.itp │ │ │ ├── POPI1_4.pdb │ │ │ └── POPI1_4_posre.itp │ │ ├── POPI1_5 │ │ │ ├── POPI1_5.itp │ │ │ ├── POPI1_5.pdb │ │ │ └── POPI1_5_posre.itp │ │ ├── POPI2_3-4_3 │ │ │ ├── POPI2_3-4_3.itp │ │ │ ├── POPI2_3-4_3.pdb │ │ │ └── POPI2_3-4_3_posre.itp │ │ ├── POPI2_3-4_4 │ │ │ ├── POPI2_3-4_4.itp │ │ │ ├── POPI2_3-4_4.pdb │ │ │ └── POPI2_3-4_4_posre.itp │ │ ├── POPI2_3-5 │ │ │ ├── POPI2_3-5.itp │ │ │ ├── POPI2_3-5.pdb │ │ │ ├── POPI2_3-5.pdb2 │ │ │ └── POPI2_3-5_posre.itp │ │ ├── POPI2_3-5_3 │ │ │ ├── POPI2_3-5_3.itp │ │ │ ├── POPI2_3-5_3.pdb │ │ │ └── POPI2_3-5_3_posre.itp │ │ ├── POPI2_3-5_5 │ │ │ ├── POPI2_3-5_5.itp │ │ │ ├── POPI2_3-5_5.pdb │ │ │ └── POPI2_3-5_5_posre.itp │ │ ├── POPI2_4-5_4 │ │ │ ├── POPI2_4-5_4.itp │ │ │ ├── POPI2_4-5_4.pdb │ │ │ ├── POPI2_4-5_4.pdb2 │ │ │ └── POPI2_4-5_4_posre.itp │ │ ├── POPI2_4-5_5 │ │ │ ├── POPI2_4-5_5.itp │ │ │ ├── POPI2_4-5_5.pdb │ │ │ ├── POPI2_4-5_5.pdb2 │ │ │ └── POPI2_4-5_5_posre.itp │ │ ├── POPI3_3-4-5 │ │ │ ├── POPI3_3-4-5.itp │ │ │ ├── POPI3_3-4-5.pdb │ │ │ └── POPI3_3-4-5_posre.itp │ │ ├── POPI3_3-4-5_3 │ │ │ ├── POPI3_3-4-5_3.itp │ │ │ ├── POPI3_3-4-5_3.pdb │ │ │ └── POPI3_3-4-5_3_posre.itp │ │ ├── POPI3_3-4-5_4 │ │ │ ├── POPI3_3-4-5_4.itp │ │ │ ├── POPI3_3-4-5_4.pdb │ │ │ └── POPI3_3-4-5_4_posre.itp │ │ ├── POPI3_3-4-5_5 │ │ │ ├── POPI3_3-4-5_5.itp │ │ │ ├── POPI3_3-4-5_5.pdb │ │ │ └── POPI3_3-4-5_5_posre.itp │ │ ├── POPS │ │ │ ├── POPS.itp │ │ │ ├── POPS.pdb │ │ │ ├── POPS.pdb2 │ │ │ └── POPS_posre.itp │ │ ├── RAMP │ │ │ ├── RAMP.itp │ │ │ ├── RAMP.pdb │ │ │ └── RAMP_posre.itp │ │ ├── REMP │ │ │ ├── REMP.itp │ │ │ ├── REMP.pdb │ │ │ └── REMP_posre.itp │ │ ├── UDP1 │ │ │ ├── UDP1.itp │ │ │ ├── UDP1.pdb │ │ │ └── UDP1_posre.itp │ │ └── UDP2 │ │ │ ├── UDP2.itp │ │ │ ├── UDP2.pdb │ │ │ └── UDP2_posre.itp │ ├── other │ │ ├── DA │ │ │ ├── DA.pdb │ │ │ └── DA.top │ │ ├── DC │ │ │ ├── DC.pdb │ │ │ └── DC.top │ │ ├── DG │ │ │ ├── DG.pdb │ │ │ └── DG.top │ │ ├── DT │ │ │ ├── DT.pdb │ │ │ └── DT.top │ │ ├── _NAG │ │ │ ├── #NAG.pdb.1# │ │ │ ├── NAG.pdb │ │ │ └── NAG.top │ │ ├── _NAM │ │ │ ├── #NAM.pdb.1# │ │ │ ├── #NAM.pdb.2# │ │ │ ├── #NAML.pdb.1# │ │ │ ├── NAM.pdb │ │ │ └── NAML.pdb │ │ ├── _PEPL │ │ │ ├── PEPL.pdb │ │ │ └── PEPL.top │ │ ├── _PEPS │ │ │ ├── PEPS.pdb │ │ │ └── PEPS.top │ │ └── _UDP2 │ │ │ └── UDP2.pdb │ ├── protein │ │ ├── ALA │ │ │ ├── ALA.pdb │ │ │ └── ALA.top │ │ ├── ARG │ │ │ ├── ARG.pdb │ │ │ └── ARG.top │ │ ├── ASN │ │ │ ├── ASN.pdb │ │ │ └── ASN.top │ │ ├── ASP │ │ │ ├── ASP.pdb │ │ │ └── ASP.top │ │ ├── CYS │ │ │ ├── CYS.pdb │ │ │ └── CYS.top │ │ ├── GLN │ │ │ ├── GLN.pdb │ │ │ └── GLN.top │ │ ├── GLU │ │ │ ├── GLU.pdb │ │ │ └── GLU.top │ │ ├── GLY │ │ │ ├── GLY.pdb │ │ │ └── GLY.top │ │ ├── HIS │ │ │ ├── HIS.pdb │ │ │ └── HIS.top │ │ ├── ILE │ │ │ ├── ILE.pdb │ │ │ └── ILE.top │ │ ├── LEU │ │ │ ├── LEU.pdb │ │ │ └── LEU.top │ │ ├── LYS │ │ │ ├── LYS.pdb │ │ │ └── LYS.top │ │ ├── MET │ │ │ ├── MET.pdb │ │ │ └── MET.top │ │ ├── PHE │ │ │ ├── PHE.pdb │ │ │ └── PHE.top │ │ ├── PRO │ │ │ ├── PRO.pdb │ │ │ └── PRO.top │ │ ├── SER │ │ │ ├── SER.pdb │ │ │ └── SER.top │ │ ├── THR │ │ │ ├── THR.pdb │ │ │ └── THR.top │ │ ├── TRP │ │ │ ├── TRP.pdb │ │ │ └── TRP.top │ │ ├── TYR │ │ │ ├── TYR.pdb │ │ │ └── TYR.top │ │ └── VAL │ │ │ ├── VAL.pdb │ │ │ └── VAL.top │ └── solvent │ │ └── W │ │ ├── SPC.itp │ │ ├── SPC.pdb │ │ ├── SPC.top │ │ ├── SPCE.itp │ │ ├── SPCE.pdb │ │ ├── SPCE.top │ │ ├── TIP3P.itp │ │ ├── TIP3P.pdb │ │ ├── TIP3P.top │ │ ├── TIP4P.itp │ │ ├── TIP4P.pdb │ │ └── TIP4P.top │ ├── martini_2-2_lipid17_port_use_at_own_risk │ ├── ions │ │ ├── CL │ │ │ ├── CL.itp │ │ │ ├── CL.pdb │ │ │ └── CL.top │ │ ├── K │ │ │ ├── K.itp │ │ │ ├── K.pdb │ │ │ └── K.top │ │ └── NA │ │ │ ├── NA.itp │ │ │ ├── NA.pdb │ │ │ └── NA.top │ ├── non_protein │ │ ├── ION │ │ │ └── ION.pdb │ │ ├── POPC │ │ │ ├── POPC.itp │ │ │ ├── POPC.pdb │ │ │ └── POPC_posre.itp │ │ └── POPE │ │ │ ├── POPE.itp │ │ │ ├── POPE.pdb │ │ │ └── POPE_posre.itp │ └── solvent │ │ └── W │ │ ├── SPC.itp │ │ ├── SPC.pdb │ │ ├── SPC.top │ │ ├── SPCE.itp │ │ ├── SPCE.pdb │ │ ├── SPCE.top │ │ ├── TIP3P.itp │ │ ├── TIP3P.pdb │ │ ├── TIP3P.top │ │ ├── TIP4P.itp │ │ ├── TIP4P.pdb │ │ └── TIP4P.top │ ├── martini_2-2_oplsaa │ └── protein │ │ ├── ALA │ │ ├── ALA.pdb │ │ └── ALA.top │ │ ├── ARG │ │ ├── ARG.pdb │ │ └── ARG.top │ │ ├── ASN │ │ ├── ASN.pdb │ │ └── ASN.top │ │ ├── ASP │ │ ├── ASP.pdb │ │ └── ASP.top │ │ ├── CYS │ │ ├── CYS.pdb │ │ └── CYS.top │ │ ├── GLN │ │ ├── GLN.pdb │ │ └── GLN.top │ │ ├── GLU │ │ ├── GLU.pdb │ │ └── GLU.top │ │ ├── GLY │ │ ├── GLY.pdb │ │ └── GLY.top │ │ ├── HIS │ │ ├── HIS.pdb │ │ └── HIS.top │ │ ├── ILE │ │ ├── ILE.pdb │ │ └── ILE.top │ │ ├── LEU │ │ ├── LEU.pdb │ │ └── LEU.top │ │ ├── LYS │ │ ├── LYS.pdb │ │ └── LYS.top │ │ ├── MET │ │ ├── MET.pdb │ │ └── MET.top │ │ ├── PHE │ │ ├── PHE.pdb │ │ └── PHE.top │ │ ├── PRO │ │ ├── PRO.pdb │ │ └── PRO.top │ │ ├── SER │ │ ├── SER.pdb │ │ └── SER.top │ │ ├── THR │ │ ├── THR.pdb │ │ └── THR.top │ │ ├── TRP │ │ ├── TRP.pdb │ │ └── TRP.top │ │ ├── TYR │ │ ├── TYR.pdb │ │ └── TYR.top │ │ └── VAL │ │ ├── VAL.pdb │ │ └── VAL.top │ ├── martini_2-2_slipids │ ├── ions │ │ ├── CL │ │ │ ├── CL.itp │ │ │ ├── CL.pdb │ │ │ └── CL.top │ │ ├── K │ │ │ ├── K.itp │ │ │ ├── K.pdb │ │ │ └── K.top │ │ └── NA │ │ │ ├── NA.itp │ │ │ ├── NA.pdb │ │ │ └── NA.top │ ├── non_protein │ │ ├── CHOL │ │ │ ├── CHOL.itp │ │ │ ├── CHOL.pdb │ │ │ ├── CHOL.top │ │ │ └── CHOL_posre.itp │ │ ├── DLPC │ │ │ ├── DLPC.itp │ │ │ ├── DLPC.pdb │ │ │ └── DLPC_posre.itp │ │ ├── DLPE │ │ │ ├── DLPE.itp │ │ │ ├── DLPE.pdb │ │ │ └── DLPE_posre.itp │ │ ├── DLPG │ │ │ ├── DLPG.itp │ │ │ ├── DLPG.pdb │ │ │ └── DLPG_posre.itp │ │ ├── DMPC │ │ │ ├── DMPC.itp │ │ │ ├── DMPC.pdb │ │ │ └── DMPC_posre.itp │ │ ├── DOPC │ │ │ ├── DOPC.itp │ │ │ ├── DOPC.pdb │ │ │ └── DOPC_posre.itp │ │ ├── DOPE │ │ │ ├── DOPE.itp │ │ │ ├── DOPE.pdb │ │ │ └── DOPE_posre.itp │ │ ├── DOPG │ │ │ ├── DOPG.itp │ │ │ ├── DOPG.pdb │ │ │ └── DOPG_posre.itp │ │ ├── DOPS │ │ │ ├── DOPS.itp │ │ │ ├── DOPS.pdb │ │ │ └── DOPS_posre.itp │ │ ├── DPPC │ │ │ ├── DPPC.itp │ │ │ ├── DPPC.pdb │ │ │ └── DPPC_posre.itp │ │ ├── DPPE │ │ │ ├── DPPE.itp │ │ │ ├── DPPE.pdb │ │ │ └── DPPE_posre.itp │ │ ├── DPPG │ │ │ ├── DPPG.itp │ │ │ ├── DPPG.pdb │ │ │ └── DPPG_posre.itp │ │ ├── POPC │ │ │ ├── POPC.itp │ │ │ ├── POPC.pdb │ │ │ └── POPC_posre.itp │ │ ├── POPE │ │ │ ├── POPE.itp │ │ │ ├── POPE.pdb │ │ │ └── POPE_posre.itp │ │ ├── POPG │ │ │ ├── POPG.itp │ │ │ ├── POPG.pdb │ │ │ └── POPG_posre.itp │ │ └── README.txt │ ├── protein │ │ ├── ALA │ │ │ ├── ALA.pdb │ │ │ └── ALA.top │ │ ├── ARG │ │ │ ├── ARG.pdb │ │ │ └── ARG.top │ │ ├── ASN │ │ │ ├── ASN.pdb │ │ │ └── ASN.top │ │ ├── ASP │ │ │ ├── ASP.pdb │ │ │ └── ASP.top │ │ ├── CYS │ │ │ ├── CYS.pdb │ │ │ └── CYS.top │ │ ├── GLN │ │ │ ├── GLN.pdb │ │ │ └── GLN.top │ │ ├── GLU │ │ │ ├── GLU.pdb │ │ │ └── GLU.top │ │ ├── GLY │ │ │ ├── GLY.pdb │ │ │ └── GLY.top │ │ ├── HIS │ │ │ ├── HIS.pdb │ │ │ └── HIS.top │ │ ├── ILE │ │ │ ├── ILE.pdb │ │ │ └── ILE.top │ │ ├── LEU │ │ │ ├── LEU.pdb │ │ │ └── LEU.top │ │ ├── LYS │ │ │ ├── LYS.pdb │ │ │ └── LYS.top │ │ ├── MET │ │ │ ├── MET.pdb │ │ │ └── MET.top │ │ ├── PHE │ │ │ ├── PHE.pdb │ │ │ └── PHE.top │ │ ├── PRO │ │ │ ├── PRO.pdb │ │ │ └── PRO.top │ │ ├── SER │ │ │ ├── SER.pdb │ │ │ └── SER.top │ │ ├── THR │ │ │ ├── THR.pdb │ │ │ └── THR.top │ │ ├── TRP │ │ │ ├── TRP.pdb │ │ │ └── TRP.top │ │ ├── TYR │ │ │ ├── TYR.pdb │ │ │ └── TYR.top │ │ └── VAL │ │ │ ├── VAL.pdb │ │ │ └── VAL.top │ └── solvent │ │ └── W │ │ ├── SPC.pdb │ │ ├── SPC.top │ │ ├── SPCE.pdb │ │ ├── SPCE.top │ │ ├── TIP3P.pdb │ │ ├── TIP3P.top │ │ ├── TIP4P.pdb │ │ ├── TIP4P.top │ │ ├── spc.itp │ │ ├── spce.itp │ │ ├── tip3p.itp │ │ └── tip4p.itp │ ├── martini_3-0_charmm36-VS │ ├── ions │ │ ├── CL │ │ │ ├── CL.itp │ │ │ ├── CL.pdb │ │ │ └── CL.top │ │ ├── K │ │ │ ├── K.itp │ │ │ ├── K.pdb │ │ │ └── K.top │ │ └── NA │ │ │ ├── NA.itp │ │ │ ├── NA.pdb │ │ │ └── NA.top │ ├── non_protein │ │ ├── CHOL │ │ │ ├── CHOL.itp │ │ │ ├── CHOL.pdb │ │ │ ├── CHOL.top │ │ │ └── CHOL_posre.itp │ │ ├── PIP2 │ │ │ ├── PIP2.itp │ │ │ ├── PIP2.pdb │ │ │ ├── PIP2.top │ │ │ └── PIP2_posre.itp │ │ ├── POPA │ │ │ ├── POPA.itp │ │ │ ├── POPA.pdb │ │ │ └── POPA_posre.itp │ │ ├── POPC │ │ │ ├── POPC.itp │ │ │ ├── POPC.pdb │ │ │ └── POPC_posre.itp │ │ ├── POPE │ │ │ ├── POPE.itp │ │ │ ├── POPE.pdb │ │ │ └── POPE_posre.itp │ │ ├── POPG │ │ │ ├── POPG.itp │ │ │ ├── POPG.pdb │ │ │ └── POPG_posre.itp │ │ ├── SPA │ │ │ ├── SPA.itp │ │ │ ├── SPA.pdb │ │ │ └── SPA_posre.itp │ │ └── SPU │ │ │ ├── SPU.itp │ │ │ ├── SPU.pdb │ │ │ └── SPU_posre.itp │ ├── protein │ │ ├── ALA │ │ │ ├── ALA.pdb │ │ │ └── ALA.top │ │ ├── ARG │ │ │ ├── ARG.pdb │ │ │ └── ARG.top │ │ ├── ASN │ │ │ ├── ASN.pdb │ │ │ └── ASN.top │ │ ├── ASP │ │ │ ├── ASP.pdb │ │ │ └── ASP.top │ │ ├── CYS │ │ │ ├── CYS.pdb │ │ │ └── CYS.top │ │ ├── GLN │ │ │ ├── GLN.pdb │ │ │ └── GLN.top │ │ ├── GLU │ │ │ ├── GLU.pdb │ │ │ └── GLU.top │ │ ├── GLY │ │ │ ├── GLY.pdb │ │ │ └── GLY.top │ │ ├── HIS │ │ │ ├── HIS.pdb │ │ │ └── HIS.top │ │ ├── ILE │ │ │ ├── ILE.pdb │ │ │ └── ILE.top │ │ ├── LEU │ │ │ ├── LEU.pdb │ │ │ └── LEU.top │ │ ├── LYS │ │ │ ├── LYS.pdb │ │ │ └── LYS.top │ │ ├── MET │ │ │ ├── MET.pdb │ │ │ └── MET.top │ │ ├── PHE │ │ │ ├── PHE.pdb │ │ │ └── PHE.top │ │ ├── PRO │ │ │ ├── PRO.pdb │ │ │ └── PRO.top │ │ ├── SER │ │ │ ├── SER.pdb │ │ │ └── SER.top │ │ ├── THR │ │ │ ├── THR.pdb │ │ │ └── THR.top │ │ ├── TRP │ │ │ ├── TRP.pdb │ │ │ └── TRP.top │ │ ├── TYR │ │ │ ├── TYR.pdb │ │ │ └── TYR.top │ │ └── VAL │ │ │ ├── VAL.pdb │ │ │ └── VAL.top │ ├── protein_modified │ │ ├── CYSD │ │ │ ├── CYSD.pdb │ │ │ └── CYSD.top │ │ ├── CYST │ │ │ ├── CYST.pdb │ │ │ └── CYST.top │ │ ├── GLYM │ │ │ ├── GLYM.pdb │ │ │ └── GLYM.top │ │ ├── GLYP │ │ │ ├── GLYP.pdb │ │ │ └── GLYP.top │ │ └── _SERP │ │ │ └── ser.pdb │ └── solvent │ │ └── W │ │ ├── SPC.itp │ │ ├── SPC.pdb │ │ ├── SPC.top │ │ ├── SPCE.itp │ │ ├── SPCE.pdb │ │ ├── SPCE.top │ │ ├── TIP3P.itp │ │ ├── TIP3P.pdb │ │ ├── TIP3P.top │ │ ├── TIP4P.itp │ │ ├── TIP4P.pdb │ │ └── TIP4P.top │ ├── martini_3-0_charmm36 │ ├── ions │ │ ├── CL │ │ │ ├── CL.itp │ │ │ ├── CL.pdb │ │ │ └── CL.top │ │ ├── K │ │ │ ├── K.itp │ │ │ ├── K.pdb │ │ │ └── K.top │ │ └── NA │ │ │ ├── NA.itp │ │ │ ├── NA.pdb │ │ │ └── NA.top │ ├── non_protein │ │ ├── 4HPA │ │ │ ├── 4HPA.itp │ │ │ ├── 4HPA.pdb │ │ │ ├── 4HPA.top │ │ │ └── 4HPA_posre.itp │ │ ├── CARD │ │ │ ├── CARD.itp │ │ │ ├── CARD.pdb │ │ │ └── CARD_posre.itp │ │ ├── CDL2 │ │ │ ├── CDL2.itp │ │ │ ├── CDL2.pdb │ │ │ └── CDL2_posre.itp │ │ ├── CHOL │ │ │ ├── CHOL.itp │ │ │ ├── CHOL.pdb │ │ │ ├── CHOL.top │ │ │ └── CHOL_posre.itp │ │ ├── DGPC │ │ │ ├── DGPC.itp │ │ │ ├── DGPC.pdb │ │ │ └── DGPC_posre.itp │ │ ├── DGPE │ │ │ ├── DGPE.itp │ │ │ ├── DGPE.pdb │ │ │ └── DGPE_posre.itp │ │ ├── DLPC │ │ │ ├── DLPC.itp │ │ │ ├── DLPC.pdb │ │ │ └── DLPC_posre.itp │ │ ├── DLPE │ │ │ ├── DLPE.itp │ │ │ ├── DLPE.pdb │ │ │ └── DLPE_posre.itp │ │ ├── DMPC │ │ │ ├── DMPC.itp │ │ │ ├── DMPC.pdb │ │ │ └── DMPC_posre.itp │ │ ├── DMPE │ │ │ ├── DMPE.itp │ │ │ ├── DMPE.pdb │ │ │ └── DMPE_posre.itp │ │ ├── DMPI │ │ │ ├── DMPI.itp │ │ │ ├── DMPI.pdb │ │ │ └── DMPI_posre.itp │ │ ├── DMPS │ │ │ ├── DMPS.itp │ │ │ ├── DMPS.pdb │ │ │ └── DMPS_posre.itp │ │ ├── DNPC │ │ │ ├── DNPC.itp │ │ │ ├── DNPC.pdb │ │ │ └── DNPC_posre.itp │ │ ├── DNPE │ │ │ ├── DNPE.itp │ │ │ ├── DNPE.pdb │ │ │ └── DNPE_posre.itp │ │ ├── DOPC │ │ │ ├── DOPC.itp │ │ │ ├── DOPC.pdb │ │ │ └── DOPC_posre.itp │ │ ├── DOPE │ │ │ ├── DOPE.itp │ │ │ ├── DOPE.pdb │ │ │ └── DOPE_posre.itp │ │ ├── DPPC │ │ │ ├── DPPC.itp │ │ │ ├── DPPC.pdb │ │ │ └── DPPC_posre.itp │ │ ├── DPPE │ │ │ ├── DPPE.itp │ │ │ ├── DPPE.pdb │ │ │ └── DPPE_posre.itp │ │ ├── DYPC │ │ │ ├── DYPC.itp │ │ │ ├── DYPC.pdb │ │ │ └── DYPC_posre.itp │ │ ├── DYPE │ │ │ ├── DYPE.itp │ │ │ ├── DYPE.pdb │ │ │ └── DYPE_posre.itp │ │ ├── HPPA │ │ │ ├── HPPA.itp │ │ │ ├── HPPA.pdb │ │ │ ├── HPPA.top │ │ │ └── HPPA_posre.itp │ │ ├── LIPA │ │ │ ├── LIPA.itp │ │ │ ├── LIPA.pdb │ │ │ └── LIPA_posre.itp │ │ ├── PCRE │ │ │ ├── PCRE.itp │ │ │ ├── PCRE.pdb │ │ │ ├── PCRE.top │ │ │ └── PCRE_posre.itp │ │ ├── PIP2 │ │ │ ├── PIP2.itp │ │ │ ├── PIP2.pdb │ │ │ └── PIP2_posre.itp │ │ ├── POPA │ │ │ ├── POPA.itp │ │ │ ├── POPA.pdb │ │ │ └── POPA_posre.itp │ │ ├── POPC │ │ │ ├── POPC.itp │ │ │ ├── POPC.pdb │ │ │ └── POPC_posre.itp │ │ ├── POPE │ │ │ ├── POPE.itp │ │ │ ├── POPE.pdb │ │ │ └── POPE_posre.itp │ │ ├── POPG │ │ │ ├── POPG.itp │ │ │ ├── POPG.pdb │ │ │ └── POPG_posre.itp │ │ ├── POPI │ │ │ ├── POPI.itp │ │ │ ├── POPI.pdb │ │ │ └── POPI_posre.itp │ │ ├── POPI1_3 │ │ │ ├── POPI1_3.itp │ │ │ ├── POPI1_3.pdb │ │ │ └── POPI1_3_posre.itp │ │ ├── POPI1_4 │ │ │ ├── POPI1_4.itp │ │ │ ├── POPI1_4.pdb │ │ │ └── POPI1_4_posre.itp │ │ ├── POPI1_5 │ │ │ ├── POPI1_5.itp │ │ │ ├── POPI1_5.pdb │ │ │ └── POPI1_5_posre.itp │ │ ├── POPI2_3-4_3 │ │ │ ├── POPI2_3-4_3.itp │ │ │ ├── POPI2_3-4_3.pdb │ │ │ └── POPI2_3-4_3_posre.itp │ │ ├── POPI2_3-4_4 │ │ │ ├── POPI2_3-4_4.itp │ │ │ ├── POPI2_3-4_4.pdb │ │ │ └── POPI2_3-4_4_posre.itp │ │ ├── POPI2_3-5 │ │ │ ├── POPI2_3-5.itp │ │ │ ├── POPI2_3-5.pdb │ │ │ └── POPI2_3-5_posre.itp │ │ ├── POPI2_3-5_3 │ │ │ ├── POPI2_3-5_3.itp │ │ │ ├── POPI2_3-5_3.pdb │ │ │ └── POPI2_3-5_3_posre.itp │ │ ├── POPI2_3-5_5 │ │ │ ├── POPI2_3-5_5.itp │ │ │ ├── POPI2_3-5_5.pdb │ │ │ └── POPI2_3-5_5_posre.itp │ │ ├── POPI2_4-5_4 │ │ │ ├── POPI2_4-5_4.itp │ │ │ ├── POPI2_4-5_4.pdb │ │ │ └── POPI2_4-5_4_posre.itp │ │ ├── POPI2_4-5_5 │ │ │ ├── POPI2_4-5_5.itp │ │ │ ├── POPI2_4-5_5.pdb │ │ │ └── POPI2_4-5_5_posre.itp │ │ ├── POPI3_3-4-5 │ │ │ ├── POPI3_3-4-5.itp │ │ │ ├── POPI3_3-4-5.pdb │ │ │ └── POPI3_3-4-5_posre.itp │ │ ├── POPI3_3-4-5_3 │ │ │ ├── POPI3_3-4-5_3.itp │ │ │ ├── POPI3_3-4-5_3.pdb │ │ │ └── POPI3_3-4-5_3_posre.itp │ │ ├── POPI3_3-4-5_4 │ │ │ ├── POPI3_3-4-5_4.itp │ │ │ ├── POPI3_3-4-5_4.pdb │ │ │ └── POPI3_3-4-5_4_posre.itp │ │ ├── POPI3_3-4-5_5 │ │ │ ├── POPI3_3-4-5_5.itp │ │ │ ├── POPI3_3-4-5_5.pdb │ │ │ └── POPI3_3-4-5_5_posre.itp │ │ ├── RAMP │ │ │ ├── RAMP.itp │ │ │ ├── RAMP.pdb │ │ │ └── RAMP_posre.itp │ │ ├── REMP │ │ │ ├── REMP.itp │ │ │ ├── REMP.pdb │ │ │ └── REMP_posre.itp │ │ ├── TMM │ │ │ ├── TMM.itp │ │ │ ├── TMM.pdb │ │ │ └── TMM_posre.itp │ │ ├── TMMA │ │ │ ├── TMMA.itp │ │ │ ├── TMMA.pdb │ │ │ └── TMMA_posre.itp │ │ └── UDP2 │ │ │ ├── UDP2.itp │ │ │ ├── UDP2.pdb │ │ │ └── UDP2_posre.itp │ ├── protein │ │ ├── ALA │ │ │ ├── ALA.pdb │ │ │ └── ALA.top │ │ ├── ARG │ │ │ ├── ARG.pdb │ │ │ └── ARG.top │ │ ├── ASN │ │ │ ├── ASN.pdb │ │ │ └── ASN.top │ │ ├── ASP │ │ │ ├── ASP.pdb │ │ │ └── ASP.top │ │ ├── CYS │ │ │ ├── CYS.pdb │ │ │ └── CYS.top │ │ ├── GLN │ │ │ ├── GLN.pdb │ │ │ └── GLN.top │ │ ├── GLU │ │ │ ├── GLU.pdb │ │ │ └── GLU.top │ │ ├── GLY │ │ │ ├── GLY.pdb │ │ │ └── GLY.top │ │ ├── HIS │ │ │ ├── HIS.pdb │ │ │ └── HIS.top │ │ ├── ILE │ │ │ ├── ILE.pdb │ │ │ └── ILE.top │ │ ├── LEU │ │ │ ├── LEU.pdb │ │ │ └── LEU.top │ │ ├── LYS │ │ │ ├── LYS.pdb │ │ │ └── LYS.top │ │ ├── MET │ │ │ ├── MET.pdb │ │ │ └── MET.top │ │ ├── PHE │ │ │ ├── PHE.pdb │ │ │ └── PHE.top │ │ ├── PRO │ │ │ ├── PRO.pdb │ │ │ └── PRO.top │ │ ├── SER │ │ │ ├── SER.pdb │ │ │ └── SER.top │ │ ├── THR │ │ │ ├── THR.pdb │ │ │ └── THR.top │ │ ├── TRP │ │ │ ├── TRP.pdb │ │ │ └── TRP.top │ │ ├── TYR │ │ │ ├── TYR.pdb │ │ │ └── TYR.top │ │ └── VAL │ │ │ ├── VAL.pdb │ │ │ └── VAL.top │ ├── protein_modified │ │ ├── CYSD │ │ │ ├── CYSD.pdb │ │ │ └── CYSD.top │ │ ├── CYST │ │ │ ├── CYST.pdb │ │ │ └── CYST.top │ │ ├── GLYM │ │ │ ├── GLYM.pdb │ │ │ └── GLYM.top │ │ ├── GLYP │ │ │ ├── GLYP.pdb │ │ │ └── GLYP.top │ │ └── _SERP │ │ │ └── ser.pdb │ └── solvent │ │ └── W │ │ ├── SPC.itp │ │ ├── SPC.pdb │ │ ├── SPC.top │ │ ├── SPCE.itp │ │ ├── SPCE.pdb │ │ ├── SPCE.top │ │ ├── TIP3P.itp │ │ ├── TIP3P.pdb │ │ ├── TIP3P.top │ │ ├── TIP4P.itp │ │ ├── TIP4P.pdb │ │ └── TIP4P.top │ ├── martini_3-0_charmm36_Jul2021 │ ├── ions │ │ ├── CL │ │ │ ├── CL.itp │ │ │ ├── CL.pdb │ │ │ └── CL.top │ │ ├── K │ │ │ ├── K.itp │ │ │ ├── K.pdb │ │ │ └── K.top │ │ └── NA │ │ │ ├── NA.itp │ │ │ ├── NA.pdb │ │ │ └── NA.top │ ├── non_protein │ │ ├── 4HPA │ │ │ ├── 4HPA.itp │ │ │ ├── 4HPA.pdb │ │ │ ├── 4HPA.top │ │ │ └── 4HPA_posre.itp │ │ ├── CARD │ │ │ ├── CARD.itp │ │ │ ├── CARD.pdb │ │ │ └── CARD_posre.itp │ │ ├── CDL2 │ │ │ ├── CDL2.itp │ │ │ ├── CDL2.pdb │ │ │ └── CDL2_posre.itp │ │ ├── CHOL │ │ │ ├── CHOL.itp │ │ │ ├── CHOL.pdb │ │ │ ├── CHOL.top │ │ │ └── CHOL_posre.itp │ │ ├── DGPC │ │ │ ├── DGPC.itp │ │ │ ├── DGPC.pdb │ │ │ └── DGPC_posre.itp │ │ ├── DGPE │ │ │ ├── DGPE.itp │ │ │ ├── DGPE.pdb │ │ │ └── DGPE_posre.itp │ │ ├── DLPC │ │ │ ├── DLPC.itp │ │ │ ├── DLPC.pdb │ │ │ └── DLPC_posre.itp │ │ ├── DLPE │ │ │ ├── DLPE.itp │ │ │ ├── DLPE.pdb │ │ │ └── DLPE_posre.itp │ │ ├── DMPC │ │ │ ├── DMPC.itp │ │ │ ├── DMPC.pdb │ │ │ └── DMPC_posre.itp │ │ ├── DMPE │ │ │ ├── DMPE.itp │ │ │ ├── DMPE.pdb │ │ │ └── DMPE_posre.itp │ │ ├── DMPI │ │ │ ├── DMPI.itp │ │ │ ├── DMPI.pdb │ │ │ └── DMPI_posre.itp │ │ ├── DMPS │ │ │ ├── DMPS.itp │ │ │ ├── DMPS.pdb │ │ │ └── DMPS_posre.itp │ │ ├── DNPC │ │ │ ├── DNPC.itp │ │ │ ├── DNPC.pdb │ │ │ └── DNPC_posre.itp │ │ ├── DNPE │ │ │ ├── DNPE.itp │ │ │ ├── DNPE.pdb │ │ │ └── DNPE_posre.itp │ │ ├── DOPC │ │ │ ├── DOPC.itp │ │ │ ├── DOPC.pdb │ │ │ └── DOPC_posre.itp │ │ ├── DOPE │ │ │ ├── DOPE.itp │ │ │ ├── DOPE.pdb │ │ │ └── DOPE_posre.itp │ │ ├── DPPC │ │ │ ├── DPPC.itp │ │ │ ├── DPPC.pdb │ │ │ └── DPPC_posre.itp │ │ ├── DPPE │ │ │ ├── DPPE.itp │ │ │ ├── DPPE.pdb │ │ │ └── DPPE_posre.itp │ │ ├── DYPC │ │ │ ├── DYPC.itp │ │ │ ├── DYPC.pdb │ │ │ └── DYPC_posre.itp │ │ ├── DYPE │ │ │ ├── DYPE.itp │ │ │ ├── DYPE.pdb │ │ │ └── DYPE_posre.itp │ │ ├── HPPA │ │ │ ├── HPPA.itp │ │ │ ├── HPPA.pdb │ │ │ ├── HPPA.top │ │ │ └── HPPA_posre.itp │ │ ├── LIPA │ │ │ ├── LIPA.itp │ │ │ ├── LIPA.pdb │ │ │ └── LIPA_posre.itp │ │ ├── PCRE │ │ │ ├── PCRE.itp │ │ │ ├── PCRE.pdb │ │ │ ├── PCRE.top │ │ │ └── PCRE_posre.itp │ │ ├── PIP2 │ │ │ ├── PIP2.itp │ │ │ ├── PIP2.pdb │ │ │ └── PIP2_posre.itp │ │ ├── POPA │ │ │ ├── POPA.itp │ │ │ ├── POPA.pdb │ │ │ └── POPA_posre.itp │ │ ├── POPC │ │ │ ├── POPC.itp │ │ │ ├── POPC.pdb │ │ │ └── POPC_posre.itp │ │ ├── POPE │ │ │ ├── POPE.itp │ │ │ ├── POPE.pdb │ │ │ └── POPE_posre.itp │ │ ├── POPG │ │ │ ├── POPG.itp │ │ │ ├── POPG.pdb │ │ │ └── POPG_posre.itp │ │ ├── POPI │ │ │ ├── POPI.itp │ │ │ ├── POPI.pdb │ │ │ └── POPI_posre.itp │ │ ├── POPI1_3 │ │ │ ├── POPI1_3.itp │ │ │ ├── POPI1_3.pdb │ │ │ └── POPI1_3_posre.itp │ │ ├── POPI1_4 │ │ │ ├── POPI1_4.itp │ │ │ ├── POPI1_4.pdb │ │ │ └── POPI1_4_posre.itp │ │ ├── POPI1_5 │ │ │ ├── POPI1_5.itp │ │ │ ├── POPI1_5.pdb │ │ │ └── POPI1_5_posre.itp │ │ ├── POPI2_3-4_3 │ │ │ ├── POPI2_3-4_3.itp │ │ │ ├── POPI2_3-4_3.pdb │ │ │ └── POPI2_3-4_3_posre.itp │ │ ├── POPI2_3-4_4 │ │ │ ├── POPI2_3-4_4.itp │ │ │ ├── POPI2_3-4_4.pdb │ │ │ └── POPI2_3-4_4_posre.itp │ │ ├── POPI2_3-5 │ │ │ ├── POPI2_3-5.itp │ │ │ ├── POPI2_3-5.pdb │ │ │ └── POPI2_3-5_posre.itp │ │ ├── POPI2_3-5_3 │ │ │ ├── POPI2_3-5_3.itp │ │ │ ├── POPI2_3-5_3.pdb │ │ │ └── POPI2_3-5_3_posre.itp │ │ ├── POPI2_3-5_5 │ │ │ ├── POPI2_3-5_5.itp │ │ │ ├── POPI2_3-5_5.pdb │ │ │ └── POPI2_3-5_5_posre.itp │ │ ├── POPI2_4-5_4 │ │ │ ├── POPI2_4-5_4.itp │ │ │ ├── POPI2_4-5_4.pdb │ │ │ └── POPI2_4-5_4_posre.itp │ │ ├── POPI2_4-5_5 │ │ │ ├── POPI2_4-5_5.itp │ │ │ ├── POPI2_4-5_5.pdb │ │ │ └── POPI2_4-5_5_posre.itp │ │ ├── POPI3_3-4-5 │ │ │ ├── POPI3_3-4-5.itp │ │ │ ├── POPI3_3-4-5.pdb │ │ │ └── POPI3_3-4-5_posre.itp │ │ ├── POPI3_3-4-5_3 │ │ │ ├── POPI3_3-4-5_3.itp │ │ │ ├── POPI3_3-4-5_3.pdb │ │ │ └── POPI3_3-4-5_3_posre.itp │ │ ├── POPI3_3-4-5_4 │ │ │ ├── POPI3_3-4-5_4.itp │ │ │ ├── POPI3_3-4-5_4.pdb │ │ │ └── POPI3_3-4-5_4_posre.itp │ │ ├── POPI3_3-4-5_5 │ │ │ ├── POPI3_3-4-5_5.itp │ │ │ ├── POPI3_3-4-5_5.pdb │ │ │ └── POPI3_3-4-5_5_posre.itp │ │ ├── POPS │ │ │ ├── POPS.itp │ │ │ ├── POPS.pdb │ │ │ ├── POPS.pdb2 │ │ │ └── POPS_posre.itp │ │ ├── RAMP │ │ │ ├── RAMP.itp │ │ │ ├── RAMP.pdb │ │ │ └── RAMP_posre.itp │ │ ├── REMP │ │ │ ├── REMP.itp │ │ │ ├── REMP.pdb │ │ │ └── REMP_posre.itp │ │ ├── SAPC │ │ │ ├── SAPC.itp │ │ │ ├── SAPC.pdb │ │ │ └── SAPC.top │ │ ├── TMM │ │ │ ├── TMM.itp │ │ │ ├── TMM.pdb │ │ │ └── TMM_posre.itp │ │ ├── TMMA │ │ │ ├── TMMA.itp │ │ │ ├── TMMA.pdb │ │ │ └── TMMA_posre.itp │ │ └── UDP2 │ │ │ ├── UDP2.itp │ │ │ ├── UDP2.pdb │ │ │ └── UDP2_posre.itp │ ├── protein │ │ ├── ALA │ │ │ ├── ALA.pdb │ │ │ └── ALA.top │ │ ├── ARG │ │ │ ├── ARG.pdb │ │ │ └── ARG.top │ │ ├── ASN │ │ │ ├── ASN.pdb │ │ │ └── ASN.top │ │ ├── ASP │ │ │ ├── ASP.pdb │ │ │ └── ASP.top │ │ ├── CYS │ │ │ ├── CYS.pdb │ │ │ └── CYS.top │ │ ├── GLN │ │ │ ├── GLN.pdb │ │ │ └── GLN.top │ │ ├── GLU │ │ │ ├── GLU.pdb │ │ │ └── GLU.top │ │ ├── GLY │ │ │ ├── GLY.pdb │ │ │ └── GLY.top │ │ ├── HIS │ │ │ ├── HIS.pdb │ │ │ └── HIS.top │ │ ├── ILE │ │ │ ├── ILE.pdb │ │ │ └── ILE.top │ │ ├── LEU │ │ │ ├── LEU.pdb │ │ │ └── LEU.top │ │ ├── LYS │ │ │ ├── LYS.pdb │ │ │ └── LYS.top │ │ ├── MET │ │ │ ├── MET.pdb │ │ │ └── MET.top │ │ ├── PHE │ │ │ ├── PHE.pdb │ │ │ └── PHE.top │ │ ├── PRO │ │ │ ├── PRO.pdb │ │ │ └── PRO.top │ │ ├── SER │ │ │ ├── SER.pdb │ │ │ └── SER.top │ │ ├── THR │ │ │ ├── THR.pdb │ │ │ └── THR.top │ │ ├── TRP │ │ │ ├── TRP.pdb │ │ │ └── TRP.top │ │ ├── TYR │ │ │ ├── TYR.pdb │ │ │ └── TYR.top │ │ └── VAL │ │ │ ├── VAL.pdb │ │ │ └── VAL.top │ └── solvent │ │ └── W │ │ ├── SPC.itp │ │ ├── SPC.pdb │ │ ├── SPC.top │ │ ├── SPCE.itp │ │ ├── SPCE.pdb │ │ ├── SPCE.top │ │ ├── TIP3P.itp │ │ ├── TIP3P.pdb │ │ ├── TIP3P.top │ │ ├── TIP4P.itp │ │ ├── TIP4P.pdb │ │ └── TIP4P.top │ ├── martini_3-0_oplsaa │ └── protein │ │ ├── ALA │ │ ├── ALA.pdb │ │ └── ALA.top │ │ ├── ARG │ │ ├── ARG.pdb │ │ └── ARG.top │ │ ├── ASN │ │ ├── ASN.pdb │ │ └── ASN.top │ │ ├── ASP │ │ ├── ASP.pdb │ │ └── ASP.top │ │ ├── CYS │ │ ├── CYS.pdb │ │ └── CYS.top │ │ ├── GLN │ │ ├── GLN.pdb │ │ └── GLN.top │ │ ├── GLU │ │ ├── GLU.pdb │ │ └── GLU.top │ │ ├── GLY │ │ ├── GLY.pdb │ │ └── GLY.top │ │ ├── HIS │ │ ├── HIS.pdb │ │ └── HIS.top │ │ ├── ILE │ │ ├── ILE.pdb │ │ └── ILE.top │ │ ├── LEU │ │ ├── LEU.pdb │ │ └── LEU.top │ │ ├── LYS │ │ ├── LYS.pdb │ │ └── LYS.top │ │ ├── MET │ │ ├── MET.pdb │ │ └── MET.top │ │ ├── PHE │ │ ├── PHE.pdb │ │ └── PHE.top │ │ ├── PRO │ │ ├── PRO.pdb │ │ └── PRO.top │ │ ├── SER │ │ ├── SER.pdb │ │ └── SER.top │ │ ├── THR │ │ ├── THR.pdb │ │ └── THR.top │ │ ├── TRP │ │ ├── TRP.pdb │ │ └── TRP.top │ │ ├── TYR │ │ ├── TYR.pdb │ │ └── TYR.top │ │ └── VAL │ │ ├── VAL.pdb │ │ └── VAL.top │ ├── martini_3-0_slipids │ ├── ions │ │ ├── CL │ │ │ ├── CL.itp │ │ │ ├── CL.pdb │ │ │ └── CL.top │ │ ├── K │ │ │ ├── K.itp │ │ │ ├── K.pdb │ │ │ └── K.top │ │ └── NA │ │ │ ├── NA.itp │ │ │ ├── NA.pdb │ │ │ └── NA.top │ ├── non_protein │ │ ├── CHOL │ │ │ ├── CHOL.itp │ │ │ ├── CHOL.pdb │ │ │ ├── CHOL.top │ │ │ └── CHOL_posre.itp │ │ ├── DLPC │ │ │ ├── DLPC.itp │ │ │ ├── DLPC.pdb │ │ │ └── DLPC_posre.itp │ │ ├── DLPE │ │ │ ├── DLPE.itp │ │ │ ├── DLPE.pdb │ │ │ └── DLPE_posre.itp │ │ ├── DLPG │ │ │ ├── DLPG.itp │ │ │ ├── DLPG.pdb │ │ │ └── DLPG_posre.itp │ │ ├── DMPC │ │ │ ├── DMPC.itp │ │ │ ├── DMPC.pdb │ │ │ └── DMPC_posre.itp │ │ ├── DOPC │ │ │ ├── DOPC.itp │ │ │ ├── DOPC.pdb │ │ │ └── DOPC_posre.itp │ │ ├── DOPE │ │ │ ├── DOPE.itp │ │ │ ├── DOPE.pdb │ │ │ └── DOPE_posre.itp │ │ ├── DOPG │ │ │ ├── DOPG.itp │ │ │ ├── DOPG.pdb │ │ │ └── DOPG_posre.itp │ │ ├── DOPS │ │ │ ├── DOPS.itp │ │ │ ├── DOPS.pdb │ │ │ └── DOPS_posre.itp │ │ ├── DPPC │ │ │ ├── DPPC.itp │ │ │ ├── DPPC.pdb │ │ │ └── DPPC_posre.itp │ │ ├── DPPE │ │ │ ├── DPPE.itp │ │ │ ├── DPPE.pdb │ │ │ └── DPPE_posre.itp │ │ ├── DPPG │ │ │ ├── DPPG.itp │ │ │ ├── DPPG.pdb │ │ │ └── DPPG_posre.itp │ │ ├── POPC │ │ │ ├── POPC.itp │ │ │ ├── POPC.pdb │ │ │ └── POPC_posre.itp │ │ ├── POPE │ │ │ ├── POPE.itp │ │ │ ├── POPE.pdb │ │ │ └── POPE_posre.itp │ │ ├── POPG │ │ │ ├── POPG.itp │ │ │ ├── POPG.pdb │ │ │ └── POPG_posre.itp │ │ └── README.txt │ ├── protein │ │ ├── ALA │ │ │ ├── ALA.pdb │ │ │ └── ALA.top │ │ ├── ARG │ │ │ ├── ARG.pdb │ │ │ └── ARG.top │ │ ├── ASN │ │ │ ├── ASN.pdb │ │ │ └── ASN.top │ │ ├── ASP │ │ │ ├── ASP.pdb │ │ │ └── ASP.top │ │ ├── CYS │ │ │ ├── CYS.pdb │ │ │ └── CYS.top │ │ ├── GLN │ │ │ ├── GLN.pdb │ │ │ └── GLN.top │ │ ├── GLU │ │ │ ├── GLU.pdb │ │ │ └── GLU.top │ │ ├── GLY │ │ │ ├── GLY.pdb │ │ │ └── GLY.top │ │ ├── HIS │ │ │ ├── HIS.pdb │ │ │ └── HIS.top │ │ ├── ILE │ │ │ ├── ILE.pdb │ │ │ └── ILE.top │ │ ├── LEU │ │ │ ├── LEU.pdb │ │ │ └── LEU.top │ │ ├── LYS │ │ │ ├── LYS.pdb │ │ │ └── LYS.top │ │ ├── MET │ │ │ ├── MET.pdb │ │ │ └── MET.top │ │ ├── PHE │ │ │ ├── PHE.pdb │ │ │ └── PHE.top │ │ ├── PRO │ │ │ ├── PRO.pdb │ │ │ └── PRO.top │ │ ├── SER │ │ │ ├── SER.pdb │ │ │ └── SER.top │ │ ├── THR │ │ │ ├── THR.pdb │ │ │ └── THR.top │ │ ├── TRP │ │ │ ├── TRP.pdb │ │ │ └── TRP.top │ │ ├── TYR │ │ │ ├── TYR.pdb │ │ │ └── TYR.top │ │ └── VAL │ │ │ ├── VAL.pdb │ │ │ └── VAL.top │ └── solvent │ │ └── W │ │ ├── SPC.pdb │ │ ├── SPC.top │ │ ├── SPCE.pdb │ │ ├── SPCE.top │ │ ├── TIP3P.pdb │ │ ├── TIP3P.top │ │ ├── TIP4P.pdb │ │ ├── TIP4P.top │ │ ├── spc.itp │ │ ├── spce.itp │ │ ├── tip3p.itp │ │ └── tip4p.itp │ └── martini_3_beta_charmm36 │ ├── ions │ ├── CL │ │ ├── CL.itp │ │ ├── CL.pdb │ │ └── CL.top │ ├── K │ │ ├── K.itp │ │ ├── K.pdb │ │ └── K.top │ └── NA │ │ ├── NA.itp │ │ ├── NA.pdb │ │ └── NA.top │ ├── non_protein │ ├── 4HPA │ │ ├── 4HPA.itp │ │ ├── 4HPA.pdb │ │ ├── 4HPA.top │ │ └── 4HPA_posre.itp │ ├── CARD │ │ ├── CARD.itp │ │ ├── CARD.pdb │ │ └── CARD_posre.itp │ ├── CDL2 │ │ ├── CDL2.itp │ │ ├── CDL2.pdb │ │ └── CDL2_posre.itp │ ├── CHOL │ │ ├── CHOL.itp │ │ ├── CHOL.pdb │ │ ├── CHOL.top │ │ └── CHOL_posre.itp │ ├── DGPC │ │ ├── DGPC.itp │ │ ├── DGPC.pdb │ │ └── DGPC_posre.itp │ ├── DGPE │ │ ├── DGPE.itp │ │ ├── DGPE.pdb │ │ └── DGPE_posre.itp │ ├── DLPC │ │ ├── DLPC.itp │ │ ├── DLPC.pdb │ │ └── DLPC_posre.itp │ ├── DLPE │ │ ├── DLPE.itp │ │ ├── DLPE.pdb │ │ └── DLPE_posre.itp │ ├── DMPC │ │ ├── DMPC.itp │ │ ├── DMPC.pdb │ │ └── DMPC_posre.itp │ ├── DMPE │ │ ├── DMPE.itp │ │ ├── DMPE.pdb │ │ └── DMPE_posre.itp │ ├── DMPI │ │ ├── DMPI.itp │ │ ├── DMPI.pdb │ │ └── DMPI_posre.itp │ ├── DMPS │ │ ├── DMPS.itp │ │ ├── DMPS.pdb │ │ └── DMPS_posre.itp │ ├── DNPC │ │ ├── DNPC.itp │ │ ├── DNPC.pdb │ │ └── DNPC_posre.itp │ ├── DNPE │ │ ├── DNPE.itp │ │ ├── DNPE.pdb │ │ └── DNPE_posre.itp │ ├── DOPC │ │ ├── DOPC.itp │ │ ├── DOPC.pdb │ │ └── DOPC_posre.itp │ ├── DOPE │ │ ├── DOPE.itp │ │ ├── DOPE.pdb │ │ └── DOPE_posre.itp │ ├── DPPC │ │ ├── DPPC.itp │ │ ├── DPPC.pdb │ │ └── DPPC_posre.itp │ ├── DPPE │ │ ├── DPPE.itp │ │ ├── DPPE.pdb │ │ └── DPPE_posre.itp │ ├── DYPC │ │ ├── DYPC.itp │ │ ├── DYPC.pdb │ │ └── DYPC_posre.itp │ ├── DYPE │ │ ├── DYPE.itp │ │ ├── DYPE.pdb │ │ └── DYPE_posre.itp │ ├── HPPA │ │ ├── HPPA.itp │ │ ├── HPPA.pdb │ │ ├── HPPA.top │ │ └── HPPA_posre.itp │ ├── LIPA │ │ ├── LIPA.itp │ │ ├── LIPA.pdb │ │ └── LIPA_posre.itp │ ├── PCRE │ │ ├── PCRE.itp │ │ ├── PCRE.pdb │ │ ├── PCRE.top │ │ └── PCRE_posre.itp │ ├── PIP2 │ │ ├── PIP2.itp │ │ ├── PIP2.pdb │ │ └── PIP2_posre.itp │ ├── POPA │ │ ├── POPA.itp │ │ ├── POPA.pdb │ │ └── POPA_posre.itp │ ├── POPC │ │ ├── POPC.itp │ │ ├── POPC.pdb │ │ └── POPC_posre.itp │ ├── POPE │ │ ├── POPE.itp │ │ ├── POPE.pdb │ │ └── POPE_posre.itp │ ├── POPG │ │ ├── POPG.itp │ │ ├── POPG.pdb │ │ └── POPG_posre.itp │ ├── POPI │ │ ├── POPI.itp │ │ ├── POPI.pdb │ │ └── POPI_posre.itp │ ├── POPI1_3 │ │ ├── POPI1_3.itp │ │ ├── POPI1_3.pdb │ │ └── POPI1_3_posre.itp │ ├── POPI1_4 │ │ ├── POPI1_4.itp │ │ ├── POPI1_4.pdb │ │ └── POPI1_4_posre.itp │ ├── POPI1_5 │ │ ├── POPI1_5.itp │ │ ├── POPI1_5.pdb │ │ └── POPI1_5_posre.itp │ ├── POPI2_3-4_3 │ │ ├── POPI2_3-4_3.itp │ │ ├── POPI2_3-4_3.pdb │ │ └── POPI2_3-4_3_posre.itp │ ├── POPI2_3-4_4 │ │ ├── POPI2_3-4_4.itp │ │ ├── POPI2_3-4_4.pdb │ │ └── POPI2_3-4_4_posre.itp │ ├── POPI2_3-5 │ │ ├── POPI2_3-5.itp │ │ ├── POPI2_3-5.pdb │ │ └── POPI2_3-5_posre.itp │ ├── POPI2_3-5_3 │ │ ├── POPI2_3-5_3.itp │ │ ├── POPI2_3-5_3.pdb │ │ └── POPI2_3-5_3_posre.itp │ ├── POPI2_3-5_5 │ │ ├── POPI2_3-5_5.itp │ │ ├── POPI2_3-5_5.pdb │ │ └── POPI2_3-5_5_posre.itp │ ├── POPI2_4-5_4 │ │ ├── POPI2_4-5_4.itp │ │ ├── POPI2_4-5_4.pdb │ │ └── POPI2_4-5_4_posre.itp │ ├── POPI2_4-5_5 │ │ ├── POPI2_4-5_5.itp │ │ ├── POPI2_4-5_5.pdb │ │ └── POPI2_4-5_5_posre.itp │ ├── POPI3_3-4-5 │ │ ├── POPI3_3-4-5.itp │ │ ├── POPI3_3-4-5.pdb │ │ └── POPI3_3-4-5_posre.itp │ ├── POPI3_3-4-5_3 │ │ ├── POPI3_3-4-5_3.itp │ │ ├── POPI3_3-4-5_3.pdb │ │ └── POPI3_3-4-5_3_posre.itp │ ├── POPI3_3-4-5_4 │ │ ├── POPI3_3-4-5_4.itp │ │ ├── POPI3_3-4-5_4.pdb │ │ └── POPI3_3-4-5_4_posre.itp │ ├── POPI3_3-4-5_5 │ │ ├── POPI3_3-4-5_5.itp │ │ ├── POPI3_3-4-5_5.pdb │ │ └── POPI3_3-4-5_5_posre.itp │ ├── RAMP │ │ ├── RAMP.itp │ │ ├── RAMP.pdb │ │ └── RAMP_posre.itp │ ├── REMP │ │ ├── REMP.itp │ │ ├── REMP.pdb │ │ └── REMP_posre.itp │ ├── TMM │ │ ├── TMM.itp │ │ ├── TMM.pdb │ │ └── TMM_posre.itp │ ├── TMMA │ │ ├── TMMA.itp │ │ ├── TMMA.pdb │ │ └── TMMA_posre.itp │ └── UDP2 │ │ ├── UDP2.itp │ │ ├── UDP2.pdb │ │ └── UDP2_posre.itp │ ├── protein │ ├── ALA │ │ ├── ALA.pdb │ │ └── ALA.top │ ├── ARG │ │ ├── ARG.pdb │ │ └── ARG.top │ ├── ASN │ │ ├── ASN.pdb │ │ └── ASN.top │ ├── ASP │ │ ├── ASP.pdb │ │ └── ASP.top │ ├── CYS │ │ ├── CYS.pdb │ │ └── CYS.top │ ├── GLN │ │ ├── GLN.pdb │ │ └── GLN.top │ ├── GLU │ │ ├── GLU.pdb │ │ └── GLU.top │ ├── GLY │ │ ├── GLY.pdb │ │ └── GLY.top │ ├── HIS │ │ ├── HIS.pdb │ │ └── HIS.top │ ├── ILE │ │ ├── ILE.pdb │ │ └── ILE.top │ ├── LEU │ │ ├── LEU.pdb │ │ └── LEU.top │ ├── LYS │ │ ├── LYS.pdb │ │ └── LYS.top │ ├── MET │ │ ├── MET.pdb │ │ └── MET.top │ ├── PHE │ │ ├── PHE.pdb │ │ └── PHE.top │ ├── PRO │ │ ├── PRO.pdb │ │ └── PRO.top │ ├── SER │ │ ├── SER.pdb │ │ └── SER.top │ ├── THR │ │ ├── THR.pdb │ │ └── THR.top │ ├── TRP │ │ ├── TRP.pdb │ │ └── TRP.top │ ├── TYR │ │ ├── TYR.pdb │ │ └── TYR.top │ └── VAL │ │ ├── VAL.pdb │ │ └── VAL.top │ ├── protein_modified │ ├── CYSD │ │ ├── CYSD.pdb │ │ └── CYSD.top │ ├── CYST │ │ ├── CYST.pdb │ │ └── CYST.top │ ├── GLYM │ │ ├── GLYM.pdb │ │ └── GLYM.top │ ├── GLYP │ │ ├── GLYP.pdb │ │ └── GLYP.top │ └── _SERP │ │ └── ser.pdb │ └── solvent │ └── W │ ├── SPC.itp │ ├── SPC.pdb │ ├── SPC.top │ ├── SPCE.itp │ ├── SPCE.pdb │ ├── SPCE.top │ ├── TIP3P.itp │ ├── TIP3P.pdb │ ├── TIP3P.top │ ├── TIP4P.itp │ ├── TIP4P.pdb │ └── TIP4P.top ├── meta.yaml ├── post-link.sh ├── tests ├── database_test │ ├── atomtypes.atp │ ├── forcefields │ │ ├── charmm36-mar2019-updated.ff │ │ │ ├── atomtypes.atp │ │ │ ├── cmap.itp │ │ │ ├── ffbonded.itp │ │ │ ├── ffbonded_UNDPP.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 │ │ │ ├── modern │ │ │ ├── nbfix.itp │ │ │ ├── old_c36_cmap.itp │ │ │ ├── spc.itp │ │ │ ├── spce.itp │ │ │ ├── tip3p.itp │ │ │ ├── tip4p.itp │ │ │ ├── to_add │ │ │ └── watermodels.dat │ │ └── empty.ff │ │ │ └── .gitignore │ ├── fragments │ │ ├── _fail │ │ │ └── .gitignore │ │ ├── test_1 │ │ │ ├── .gitignore │ │ │ ├── ions │ │ │ │ ├── CL │ │ │ │ │ ├── CL.itp │ │ │ │ │ ├── CL.pdb │ │ │ │ │ └── CL.top │ │ │ │ ├── K │ │ │ │ │ ├── K.itp │ │ │ │ │ ├── K.pdb │ │ │ │ │ └── K.top │ │ │ │ └── NA │ │ │ │ │ ├── NA.itp │ │ │ │ │ ├── NA.pdb │ │ │ │ │ └── NA.top │ │ │ ├── non_protein │ │ │ │ ├── .gitignore │ │ │ │ └── CHOL │ │ │ │ │ ├── CHOL.itp │ │ │ │ │ ├── CHOL.pdb │ │ │ │ │ ├── CHOL.top │ │ │ │ │ └── CHOL_posre.itp │ │ │ ├── other │ │ │ │ └── .gitignore │ │ │ ├── protein │ │ │ │ └── PHE │ │ │ │ │ ├── PHE.pdb │ │ │ │ │ └── PHE.top │ │ │ ├── protein_modified │ │ │ │ └── .gitignore │ │ │ └── solvent │ │ │ │ └── W │ │ │ │ ├── SPC.itp │ │ │ │ ├── SPC.pdb │ │ │ │ ├── SPC.top │ │ │ │ ├── SPCE.itp │ │ │ │ ├── SPCE.pdb │ │ │ │ ├── SPCE.top │ │ │ │ ├── TIP3P.itp │ │ │ │ ├── TIP3P.pdb │ │ │ │ ├── TIP3P.top │ │ │ │ ├── TIP4P.itp │ │ │ │ ├── TIP4P.pdb │ │ │ │ └── TIP4P.top │ │ └── test_2 │ │ │ ├── .gitignore │ │ │ └── protein │ │ │ └── PHE │ │ │ ├── PHE.pdb │ │ │ └── PHE.top │ ├── test_clean │ │ ├── MIN │ │ │ └── .gitignore │ │ ├── test_tem.pdb │ │ ├── test_tem.tpr │ │ ├── test_temp.pdb │ │ └── test_temp.tpr │ └── test_correct.pdb ├── inputs │ ├── AT │ │ └── AT_INPUT_long.pdb │ └── CG │ │ └── CG_INPUT.pdb └── test.py └── tutorials ├── WZM_tutorial └── input_files │ ├── AT_0.pdb │ ├── AT_1.pdb │ ├── AT_2.pdb │ ├── AT_3.pdb │ ├── AT_input.pdb │ ├── CG_input.pdb │ └── martini_2-2_charmm36 │ ├── non_protein │ ├── ATP │ │ ├── ATP.itp │ │ ├── ATP.pdb │ │ ├── ATP.top │ │ └── ATP_posre.itp │ ├── CARD │ │ ├── CARD.itp │ │ ├── CARD.pdb │ │ └── CARD_posre.itp │ ├── CHOL │ │ ├── CHOL.itp │ │ ├── CHOL.pdb │ │ ├── CHOL.top │ │ └── CHOL_posre.itp │ ├── DGPA │ │ ├── DGPA.itp │ │ ├── DGPA.pdb │ │ └── DGPA_posre.itp │ ├── DGPC │ │ ├── DGPC.itp │ │ ├── DGPC.pdb │ │ └── DGPC_posre.itp │ ├── DGPE │ │ ├── DGPE.itp │ │ ├── DGPE.pdb │ │ ├── DGPE.pdb2 │ │ └── DGPE_posre.itp │ ├── DGPS │ │ ├── DGPS.itp │ │ ├── DGPS.pdb │ │ └── DGPS_posre.itp │ ├── DLPA │ │ ├── DLPA.itp │ │ ├── DLPA.pdb │ │ └── DLPA_posre.itp │ ├── DLPC │ │ ├── DLPC.itp │ │ ├── DLPC.pdb │ │ └── DLPC_posre.itp │ ├── DLPE │ │ ├── DLPE.itp │ │ ├── DLPE.pdb │ │ └── DLPE_posre.itp │ ├── DLPG │ │ ├── DLPG.itp │ │ ├── DLPG.pdb │ │ └── DLPG_posre.itp │ ├── DLPS │ │ ├── DLPS.itp │ │ ├── DLPS.pdb │ │ └── DLPS_posre.itp │ ├── DMPC │ │ ├── DMPC.itp │ │ ├── DMPC.pdb │ │ └── DMPC_posre.itp │ ├── DMPE │ │ ├── DMPE.itp │ │ ├── DMPE.pdb │ │ └── DMPE_posre.itp │ ├── DMPI │ │ ├── DMPI.itp │ │ ├── DMPI.pdb │ │ └── DMPI_posre.itp │ ├── DMPS │ │ ├── DMPS.itp │ │ ├── DMPS.pdb │ │ └── DMPS_posre.itp │ ├── DNPA │ │ ├── DNPA.itp │ │ ├── DNPA.pdb │ │ └── DNPA_posre.itp │ ├── DNPC │ │ ├── DNPC.itp │ │ ├── DNPC.pdb │ │ └── DNPC_posre.itp │ ├── DNPE │ │ ├── DNPE.itp │ │ ├── DNPE.pdb │ │ └── DNPE_posre.itp │ ├── DNPG │ │ ├── DNPG.itp │ │ ├── DNPG.pdb │ │ └── DNPG_posre.itp │ ├── DNPS │ │ ├── DNPS.itp │ │ ├── DNPS.pdb │ │ └── DNPS_posre.itp │ ├── DOPA │ │ ├── DOPA.itp │ │ ├── DOPA.pdb │ │ └── DOPA_posre.itp │ ├── DOPC │ │ ├── DOPC.itp │ │ ├── DOPC.pdb │ │ └── DOPC_posre.itp │ ├── DOPE │ │ ├── DOPE.itp │ │ ├── DOPE.pdb │ │ └── DOPE_posre.itp │ ├── DOPG │ │ ├── DOPG.itp │ │ ├── DOPG.pdb │ │ └── DOPG_posre.itp │ ├── DOPS │ │ ├── DOPS.itp │ │ ├── DOPS.pdb │ │ └── DOPS_posre.itp │ ├── DPG1 │ │ ├── .DS_Store │ │ ├── DPG1.itp │ │ ├── DPG1.pdb │ │ └── DPG1_posre.itp │ ├── DPG3 │ │ ├── DPG3.itp │ │ ├── DPG3.pdb │ │ └── DPG3_posre.itp │ ├── DPPA │ │ ├── DPPA.itp │ │ ├── DPPA.pdb │ │ └── DPPA_posre.itp │ ├── DPPC │ │ ├── DPPC.itp │ │ ├── DPPC.pdb │ │ └── DPPC_posre.itp │ ├── DPPE │ │ ├── DPPE.itp │ │ ├── DPPE.pdb │ │ └── DPPE_posre.itp │ ├── DPPG │ │ ├── DPPG.itp │ │ ├── DPPG.pdb │ │ └── DPPG_posre.itp │ ├── DPPS │ │ ├── DPPS.itp │ │ ├── DPPS.pdb │ │ └── DPPS_posre.itp │ ├── DYPA │ │ ├── DYPA.itp │ │ ├── DYPA.pdb │ │ └── DYPA_posre.itp │ ├── DYPC │ │ ├── DYPC.itp │ │ ├── DYPC.pdb │ │ └── DYPC_posre.itp │ ├── DYPE │ │ ├── DYPE.itp │ │ ├── DYPE.pdb │ │ └── DYPE_posre.itp │ ├── DYPG │ │ ├── DYPG.itp │ │ ├── DYPG.pdb │ │ └── DYPG_posre.itp │ ├── DYPS │ │ ├── DYPS.itp │ │ ├── DYPS.pdb │ │ └── DYPS_posre.itp │ ├── FEN │ │ ├── FEN.itp │ │ ├── FEN.pdb │ │ ├── FEN.top │ │ └── FEN_posre.itp │ ├── ION │ │ ├── ION.itp │ │ └── ION.pdb │ ├── LIPA │ │ ├── LIPA.itp │ │ ├── LIPA.pdb │ │ ├── LIPA.top │ │ └── LIPA_posre.itp │ ├── OANT │ │ ├── OANT.itp │ │ ├── OANT.pdb │ │ ├── OANT.top │ │ └── OANT_posre.itp │ ├── PIP2 │ │ ├── PIP2.itp │ │ ├── PIP2.pdb │ │ ├── PIP2.top │ │ └── PIP2_posre.itp │ ├── PIP3 │ │ ├── PIP3.itp │ │ ├── PIP3.pdb │ │ ├── PIP3.pdb2 │ │ ├── PIP3.top │ │ └── PIP3_posre.itp │ ├── POP2 │ │ ├── POP2.itp │ │ ├── POP2.pdb │ │ └── POP2_posre.itp │ ├── POPA │ │ ├── POPA.itp │ │ ├── POPA.pdb │ │ └── POPA_posre.itp │ ├── POPC │ │ ├── POPC.itp │ │ ├── POPC.pdb │ │ ├── POPC.top │ │ └── POPC_posre.itp │ ├── POPE │ │ ├── POPE.itp │ │ ├── POPE.pdb │ │ └── POPE_posre.itp │ ├── POPG │ │ ├── POPG.itp │ │ ├── POPG.pdb │ │ └── POPG_posre.itp │ ├── POPI │ │ ├── POPI.itp │ │ ├── POPI.pdb │ │ ├── POPI.pdb2 │ │ ├── POPI.top │ │ └── POPI_posre.itp │ ├── POPI1_3 │ │ ├── POPI1_3.itp │ │ ├── POPI1_3.pdb │ │ ├── POPI1_3.top │ │ └── POPI1_3_posre.itp │ ├── POPI1_4 │ │ ├── POPI1_4.itp │ │ ├── POPI1_4.pdb │ │ ├── POPI1_4.top │ │ └── POPI1_4_posre.itp │ ├── POPI1_5 │ │ ├── POPI1_5.itp │ │ ├── POPI1_5.pdb │ │ ├── POPI1_5.top │ │ └── POPI1_5_posre.itp │ ├── POPI2_3-4_3 │ │ ├── POPI2_3-4_3.itp │ │ ├── POPI2_3-4_3.pdb │ │ ├── POPI2_3-4_3.top │ │ └── POPI2_3-4_3_posre.itp │ ├── POPI2_3-4_4 │ │ ├── POPI2_3-4_4.itp │ │ ├── POPI2_3-4_4.pdb │ │ ├── POPI2_3-4_4.top │ │ └── POPI2_3-4_4_posre.itp │ ├── POPI2_3-5 │ │ ├── POPI2_3-5.itp │ │ ├── POPI2_3-5.pdb │ │ ├── POPI2_3-5.pdb2 │ │ ├── POPI2_3-5.top │ │ └── POPI2_3-5_posre.itp │ ├── POPI2_3-5_3 │ │ ├── POPI2_3-5_3.itp │ │ ├── POPI2_3-5_3.pdb │ │ ├── POPI2_3-5_3.top │ │ └── POPI2_3-5_3_posre.itp │ ├── POPI2_3-5_5 │ │ ├── POPI2_3-5_5.itp │ │ ├── POPI2_3-5_5.pdb │ │ ├── POPI2_3-5_5.top │ │ └── POPI2_3-5_5_posre.itp │ ├── POPI2_4-5_4 │ │ ├── POPI2_4-5_4.itp │ │ ├── POPI2_4-5_4.pdb │ │ ├── POPI2_4-5_4.pdb2 │ │ ├── POPI2_4-5_4.top │ │ └── POPI2_4-5_4_posre.itp │ ├── POPI2_4-5_5 │ │ ├── POPI2_4-5_5.itp │ │ ├── POPI2_4-5_5.pdb │ │ ├── POPI2_4-5_5.pdb2 │ │ ├── POPI2_4-5_5.top │ │ └── POPI2_4-5_5_posre.itp │ ├── POPI3_3-4-5 │ │ ├── POPI3_3-4-5.itp │ │ ├── POPI3_3-4-5.pdb │ │ ├── POPI3_3-4-5.top │ │ └── POPI3_3-4-5_posre.itp │ ├── POPI3_3-4-5_3 │ │ ├── POPI3_3-4-5_3.itp │ │ ├── POPI3_3-4-5_3.pdb │ │ ├── POPI3_3-4-5_3.top │ │ └── POPI3_3-4-5_3_posre.itp │ ├── POPI3_3-4-5_4 │ │ ├── POPI3_3-4-5_4.itp │ │ ├── POPI3_3-4-5_4.pdb │ │ ├── POPI3_3-4-5_4.top │ │ └── POPI3_3-4-5_4_posre.itp │ ├── POPI3_3-4-5_5 │ │ ├── POPI3_3-4-5_5.itp │ │ ├── POPI3_3-4-5_5.pdb │ │ ├── POPI3_3-4-5_5.top │ │ └── POPI3_3-4-5_5_posre.itp │ ├── POPS │ │ ├── POPS.itp │ │ ├── POPS.pdb │ │ ├── POPS.pdb2 │ │ └── POPS_posre.itp │ ├── RAMP │ │ ├── RAMP.itp │ │ ├── RAMP.pdb │ │ ├── RAMP.top │ │ └── RAMP_posre.itp │ ├── REMP │ │ ├── REMP.itp │ │ ├── REMP.pdb │ │ ├── REMP.top │ │ └── REMP_posre.itp │ ├── SOL │ │ ├── SOL.pdb │ │ ├── spc.itp │ │ ├── spce.itp │ │ ├── tip3p.itp │ │ └── tip4p.itp │ └── UDP2 │ │ ├── UDP2.itp │ │ ├── UDP2.pdb │ │ └── UDP2_posre.itp │ └── protein │ ├── ALA │ ├── ALA.pdb │ └── ALA.top │ ├── ARG │ ├── ARG.pdb │ └── ARG.top │ ├── ASN │ ├── ASN.pdb │ └── ASN.top │ ├── ASP │ ├── ASP.pdb │ └── ASP.top │ ├── CYS │ ├── CYS.pdb │ └── CYS.top │ ├── GLN │ ├── GLN.pdb │ └── GLN.top │ ├── GLU │ ├── GLU.pdb │ └── GLU.top │ ├── GLY │ ├── GLY.pdb │ └── GLY.top │ ├── HIS │ ├── HIS.pdb │ └── HIS.top │ ├── ILE │ ├── ILE.pdb │ └── ILE.top │ ├── LEU │ ├── LEU.pdb │ └── LEU.top │ ├── LYS │ ├── LYS.pdb │ └── LYS.top │ ├── MET │ ├── MET.pdb │ └── MET.top │ ├── MOD │ ├── CYSD │ │ ├── 5_bead_chain_A │ │ │ ├── BB.pdb │ │ │ ├── BIS.pdb │ │ │ ├── C1A.pdb │ │ │ ├── C1B.pdb │ │ │ ├── C2B.pdb │ │ │ ├── C3A.pdb │ │ │ ├── C3B.pdb │ │ │ ├── C4A.pdb │ │ │ ├── C4B.pdb │ │ │ ├── D2A.pdb │ │ │ ├── GL1.pdb │ │ │ ├── GL2.pdb │ │ │ ├── SC1.pdb │ │ │ └── SID.pdb │ │ ├── CYSD.pdb │ │ └── CYSD.top │ ├── CYST │ │ ├── 5_bead_A_chain │ │ │ ├── C1A.pdb │ │ │ ├── C1B.pdb │ │ │ ├── C1C.pdb │ │ │ ├── C2B.pdb │ │ │ ├── C2C.pdb │ │ │ ├── C3A.pdb │ │ │ ├── C3B.pdb │ │ │ ├── C3C.pdb │ │ │ ├── C4A.pdb │ │ │ ├── C4B.pdb │ │ │ ├── C4C.pdb │ │ │ └── D2A.pdb │ │ ├── CYST.pdb │ │ └── CYST.top │ └── _SERP │ │ └── ser.pdb │ ├── PHE │ ├── PHE.pdb │ └── PHE.top │ ├── PRO │ ├── PRO.pdb │ └── PRO.top │ ├── SER │ ├── SER.pdb │ └── SER.top │ ├── THR │ ├── THR.pdb │ └── THR.top │ ├── TRP │ ├── TRP.pdb │ └── TRP.top │ ├── TYR │ ├── TYR.pdb │ └── TYR.top │ ├── VAL │ ├── VAL.pdb │ └── VAL.top │ ├── _ACE │ └── ACE.pdb │ ├── _NME │ └── NME.pdb │ ├── _test │ ├── conf.gro │ ├── posre.itp │ ├── residues.pdb │ ├── test.pdb │ └── topol.top │ ├── residues.pdb │ └── top ├── lspa_tutorial └── input_files │ ├── AT_input.pdb │ └── CG_input.pdb ├── tutorial_1.odt └── tutorial_2.odt /.codecov.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/owenvickery/cg2at/HEAD/.codecov.yml -------------------------------------------------------------------------------- /.github/workflows/codeql-analysis.yml: 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