├── .gitignore ├── AUTHORS.rst ├── CONTRIBUTING.rst ├── HISTORY.rst ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── authors.rst ├── conf.py ├── contributing.rst ├── history.rst ├── index.rst ├── installation.rst ├── make.bat └── usage.rst ├── pytopol ├── __init__.py ├── general │ ├── __init__.py │ └── utils.py └── parsers │ ├── __init__.py │ ├── blocks.py │ ├── charmmpar.py │ ├── grotop.py │ ├── par.py │ ├── pdb.py │ ├── psf.py │ └── utils.py ├── requirements.txt ├── scripts └── psf2top.py ├── setup.py └── test ├── __init__.py ├── config.py ├── data ├── par │ ├── par_all27_prot_lipid.prm │ ├── par_all36_lipid.prm │ └── par_all36_prot.prm └── pdb │ ├── 2M0Z.pdb │ └── popc.pdb ├── profile ├── profile.py └── ref.prof ├── systems ├── README.md ├── _config.py ├── cmp_namd_gmx.py ├── glucl │ ├── glucl.pdb │ ├── glucl_autopsf.pdb │ └── glucl_autopsf.psf ├── ligand │ ├── chol_nowat.pdb │ ├── chol_nowat_autopsf.pdb │ └── chol_nowat_autopsf.psf ├── membrane │ ├── dopc.pdb │ ├── dopc_autopsf.pdb │ ├── dopc_autopsf.psf │ ├── popc.pdb │ ├── popc_autopsf.pdb │ └── popc_autopsf.psf ├── other │ ├── onlywater.pdb │ ├── onlywater_autopsf.pdb │ ├── onlywater_autopsf.psf │ ├── wat.pdb │ ├── wat_autopsf.pdb │ ├── wat_autopsf.psf │ ├── wmol.pdb │ ├── wmol_autopsf.pdb │ └── wmol_autopsf.psf ├── par │ ├── par_all27_prot_lipid.prm │ ├── par_all36_cgenff.prm │ ├── par_all36_lipid.prm │ ├── par_all36_prot.prm │ ├── par_chol.par │ ├── par_wation.par │ └── toppar_all36_lipid_cholesterol.str ├── peptide │ ├── p1_A.pdb │ ├── p1_A_autopsf.pdb │ ├── p1_A_autopsf.psf │ ├── p1_P.pdb │ ├── p1_P_autopsf.pdb │ ├── p1_P_autopsf.psf │ ├── p2_AD.pdb │ ├── p2_AD_autopsf.pdb │ ├── p2_AD_autopsf.psf │ ├── p2_AR.pdb │ ├── p2_AR_autopsf.pdb │ ├── p2_AR_autopsf.psf │ ├── p3_ADL.pdb │ ├── p3_ADL_autopsf.pdb │ ├── p3_ADL_autopsf.psf │ ├── p3_ARP.pdb │ ├── p3_ARP_autopsf.pdb │ ├── p3_ARP_autopsf.psf │ ├── p3_GPG.pdb │ ├── p3_GPG_autopsf.pdb │ ├── p3_GPG_autopsf.psf │ ├── p4_ADLK.pdb │ ├── 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