├── .gitattributes ├── .github └── workflows │ ├── check_acpype.yml │ └── codeql-analysis.yml ├── .gitignore ├── .pre-commit-config.yaml ├── .readthedocs.yaml ├── .vscode └── settings.json ├── Acpype_API_Jupyter.ipynb ├── CONTRIBUTING.md ├── Dockerfile ├── FUNDING.yml ├── LICENSE ├── MANIFEST.in ├── NOTE.txt ├── README.md ├── _config.yml ├── acpype ├── __init__.py ├── acs_api.py ├── amber_linux │ ├── GNU_LGPL_v3 │ ├── LICENSE │ ├── amber.sh │ ├── bin │ │ ├── am1bcc │ │ ├── antechamber │ │ ├── atomtype │ │ ├── bondtype │ │ ├── charmmgen │ │ ├── parmchk2 │ │ ├── sqm │ │ ├── teLeap │ │ ├── tleap │ │ └── wrapped_progs │ │ │ ├── am1bcc │ │ │ ├── antechamber │ │ │ ├── atomtype │ │ │ ├── bondtype │ │ │ └── parmchk2 │ ├── dat │ │ ├── antechamber │ │ │ ├── APS.DAT │ │ │ ├── ATCOR.DAT │ │ │ ├── ATOMTYPE_AMBER.DEF │ │ │ ├── ATOMTYPE_BCC.DEF │ │ │ ├── ATOMTYPE_CHECK.TAB │ │ │ ├── ATOMTYPE_GAS.DEF │ │ │ ├── ATOMTYPE_GFF.DEF │ │ │ ├── ATOMTYPE_GFF2.DEF │ │ │ ├── ATOMTYPE_SYBYL.DEF │ │ │ ├── ATOM_EQU.TYPE │ │ │ ├── BCCPARM.DAT │ │ │ ├── BONDTYPE_CHECK.TAB │ │ │ ├── CONNECT.TPL │ │ │ ├── CORR_NAME_TYPE.DAT │ │ │ ├── ESPPARM.DAT │ │ │ ├── GASPARM.DAT │ │ │ ├── PARMCHK.DAT │ │ │ ├── PARM_BLBA_GAFF.DAT │ │ │ ├── PARM_BLBA_GAFF2.DAT │ │ │ ├── RADIUS.DAT │ │ │ ├── database_sample.def │ │ │ ├── mainchain_sample.dat │ │ │ ├── residuegen_sample.dat │ │ │ └── respgen_addfile_sample.dat │ │ ├── chamber │ │ │ ├── par_all22_prot.inp │ │ │ ├── par_all22_sugar.inp │ │ │ ├── par_all27_prot_na.prm │ │ │ ├── par_all36_carb.prm │ │ │ ├── par_all36_prot.prm │ │ │ ├── top_all22_prot.inp │ │ │ ├── top_all22_sugar.inp │ │ │ ├── top_all27_prot_na.rtf │ │ │ ├── top_all36_carb.rtf │ │ │ ├── top_all36_prot.rtf │ │ │ └── toppar_water_ions.str │ │ └── leap │ │ │ ├── cmd │ │ │ ├── leaprc.DNA.OL15 │ │ │ ├── leaprc.DNA.OL21 │ │ │ ├── leaprc.DNA.bsc1 │ │ │ ├── leaprc.GLYCAM_06EPb │ │ │ ├── leaprc.GLYCAM_06j-1 │ │ │ ├── leaprc.RNA.LJbb │ │ │ ├── leaprc.RNA.OL3 │ │ │ ├── leaprc.RNA.ROC │ │ │ ├── leaprc.RNA.Shaw │ │ │ ├── leaprc.RNA.YIL │ │ │ ├── leaprc.amberdyes │ │ │ ├── leaprc.conste │ │ │ ├── leaprc.constph │ │ │ ├── leaprc.ffAM1 │ │ │ ├── leaprc.ffPM3 │ │ │ ├── leaprc.fluorine.ff15ipq │ │ │ ├── leaprc.gaff │ │ │ ├── leaprc.gaff2 │ │ │ ├── leaprc.lipid21 │ │ │ ├── leaprc.mimetic.ff15ipq │ │ │ ├── leaprc.modrna08 │ │ │ ├── leaprc.music │ │ │ ├── leaprc.phosaa10 │ │ │ ├── leaprc.phosaa14SB │ │ │ ├── leaprc.phosaa19SB │ │ │ ├── leaprc.phosfb18 │ │ │ ├── leaprc.protein.fb15 │ │ │ ├── leaprc.protein.ff03.r1 │ │ │ ├── leaprc.protein.ff03ua │ │ │ ├── leaprc.protein.ff14SB │ │ │ ├── leaprc.protein.ff14SB_modAA │ │ │ ├── leaprc.protein.ff14SBonlysc │ │ │ ├── leaprc.protein.ff15ipq │ │ │ ├── leaprc.protein.ff15ipq-vac │ │ │ ├── leaprc.protein.ff19SB │ │ │ ├── leaprc.protein.ff19SB_modAA │ │ │ ├── leaprc.protein.ff19ipq │ │ │ ├── leaprc.water.fb3 │ │ │ ├── leaprc.water.fb3mod │ │ │ ├── leaprc.water.fb4 │ │ │ ├── leaprc.water.opc │ │ │ ├── leaprc.water.opc3 │ │ │ ├── leaprc.water.opc3pol │ │ │ ├── leaprc.water.spce │ │ │ ├── leaprc.water.spceb │ │ │ ├── leaprc.water.tip3p │ │ │ ├── leaprc.water.tip4pd │ │ │ ├── leaprc.water.tip4pd-a99SBdisp │ │ │ ├── leaprc.water.tip4pew │ │ │ ├── leaprc.xFPchromophores │ │ │ └── oldff │ │ │ │ ├── leaprc.DNA.bsc0 │ │ │ │ ├── leaprc.GLYCAM_04 │ │ │ │ ├── leaprc.GLYCAM_06 │ │ │ │ ├── leaprc.GLYCAM_06EP │ │ │ │ ├── leaprc.GLYCAM_06h │ │ │ │ ├── leaprc.GLYCAM_06h-1 │ │ │ │ ├── leaprc.GLYCAM_06h-12SB │ │ │ │ ├── leaprc.GLYCAM_06j_10 │ │ │ │ ├── leaprc.ff02 │ │ │ │ ├── leaprc.ff02pol.r0 │ │ │ │ ├── leaprc.ff02pol.r1 │ │ │ │ ├── leaprc.ff02polEP.r0 │ │ │ │ ├── leaprc.ff02polEP.r1 │ │ │ │ ├── leaprc.ff03 │ │ │ │ ├── leaprc.ff10 │ │ │ │ ├── leaprc.ff14SB │ │ │ │ ├── leaprc.ff14SB.redq │ │ │ │ ├── leaprc.ff14ipq │ │ │ │ ├── leaprc.ff84 │ │ │ │ ├── leaprc.ff86 │ │ │ │ ├── leaprc.ff94 │ │ │ │ ├── leaprc.ff94.nmr │ │ │ │ ├── leaprc.ff96 │ │ │ │ ├── leaprc.ff98 │ │ │ │ ├── leaprc.ff99 │ │ │ │ ├── leaprc.ff99SB │ │ │ │ ├── leaprc.ff99SBildn │ │ │ │ ├── leaprc.ff99SBnmr │ │ │ │ ├── leaprc.ff99bsc0 │ │ │ │ ├── leaprc.lipid11 │ │ │ │ ├── leaprc.lipid14 │ │ │ │ ├── leaprc.lipid17 │ │ │ │ ├── leaprc.parmbsc0_chiOL4_ezOL1 │ │ │ │ ├── leaprc.rna.ff02 │ │ │ │ ├── leaprc.rna.ff02EP │ │ │ │ ├── leaprc.rna.ff84 │ │ │ │ ├── leaprc.rna.ff94 │ │ │ │ ├── leaprc.rna.ff98 │ │ │ │ ├── leaprc.rna.ff99 │ │ │ │ └── leaprc.toyrna │ │ │ ├── lib │ │ │ ├── 8Murea.readme │ │ │ ├── 8Mureabox.off │ │ │ ├── DNA.OL15.lib │ │ │ ├── DNA_CI.lib │ │ │ ├── GLYCAM_amino_06j_12SB.lib │ │ │ ├── GLYCAM_aminoct_06j_12SB.lib │ │ │ ├── GLYCAM_aminont_06j_12SB.lib │ │ │ ├── Makefile │ │ │ ├── RNA.YIL.lib │ │ │ ├── RNA.lib │ │ │ ├── RNA_CI.lib │ │ │ ├── RNA_Shaw.lib │ │ │ ├── all_amino03.lib │ │ │ ├── all_amino94.lib │ │ │ ├── all_amino94.nmr.lib │ │ │ ├── all_amino94ildn.lib │ │ │ ├── all_aminoAM1.lib │ │ │ ├── all_aminoPM3.lib │ │ │ ├── all_aminoct03.lib │ │ │ ├── all_aminoct94.lib │ │ │ ├── all_aminoct94ildn.lib │ │ │ ├── all_aminoctfb15.lib │ │ │ ├── all_aminofb15.lib │ │ │ ├── all_aminont03.lib │ │ │ ├── all_aminont94.lib │ │ │ ├── all_aminont94ildn.lib │ │ │ ├── all_aminontfb15.lib │ │ │ ├── all_modrna08.lib │ │ │ ├── all_nucleic94.lib │ │ │ ├── all_nucleic94.nmr.lib │ │ │ ├── all_prot_nucleic10.cmd │ │ │ ├── all_prot_nucleic10.lib │ │ │ ├── amberdyes.lib │ │ │ ├── amino10.lib │ │ │ ├── amino12.lib │ │ │ ├── amino12.redq.lib │ │ │ ├── amino14ipq.lib │ │ │ ├── amino15ipq-vac_10.0.lib │ │ │ ├── amino15ipq_10.0.lib │ │ │ ├── amino19.lib │ │ │ ├── amino19ipq_0.9.lib │ │ │ ├── amino19ipq_0.9_pol.lib │ │ │ ├── amino19ipq_0.9_vac.lib │ │ │ ├── aminocn15ipq_10.0.lib │ │ │ ├── aminoct10.lib │ │ │ ├── aminoct12.lib │ │ │ ├── aminoct12.redq.lib │ │ │ ├── aminoct14ipq.lib │ │ │ ├── aminoct15ipq-vac_10.0.lib │ │ │ ├── aminoct15ipq_10.0.lib │ │ │ ├── aminoct19ipq_0.9.lib │ │ │ ├── aminoct19ipq_0.9_pol.lib │ │ │ ├── aminoct19ipq_0.9_vac.lib │ │ │ ├── aminont10.lib │ │ │ ├── aminont12.lib │ │ │ ├── aminont12.redq.lib │ │ │ ├── aminont14ipq.lib │ │ │ ├── aminont15ipq-vac_10.0.lib │ │ │ ├── aminont15ipq_10.0.lib │ │ │ ├── aminont19ipq_0.9.lib │ │ │ ├── aminont19ipq_0.9_pol.lib │ │ │ ├── aminont19ipq_0.9_vac.lib │ │ │ ├── atomic_ions.cmd │ │ │ ├── atomic_ions.lib │ │ │ ├── chcl3box.off │ │ │ ├── conste.lib │ │ │ ├── constph.lib │ │ │ ├── cph_nucleic_caps.lib │ │ │ ├── fb3box.off │ │ │ ├── fb4box.off │ │ │ ├── ff-nucleic-OL21.lib │ │ │ ├── ff03.cmd │ │ │ ├── ff03ua.cmd │ │ │ ├── ff10.cmd │ │ │ ├── ff12SB.cmd │ │ │ ├── ff15ipq-19F.lib │ │ │ ├── ff15ipq-m.lib │ │ │ ├── ff94.cmd │ │ │ ├── ions94.cmd │ │ │ ├── ions94.lib │ │ │ ├── lipid21.lib │ │ │ ├── meohbox.off │ │ │ ├── mk_nablib.cmd │ │ │ ├── mod_amino.lib │ │ │ ├── mod_amino19.lib │ │ │ ├── music.lib │ │ │ ├── nab.lib │ │ │ ├── nmabox.off │ │ │ ├── nucleic10.lib │ │ │ ├── nucleic12.LJbb-RNA.lib │ │ │ ├── nucleic12.ROC-RNA.lib │ │ │ ├── nucleic12.lib │ │ │ ├── nucleic12.redq.lib │ │ │ ├── oldff │ │ │ │ ├── GLYCAM_amino_06j_10.lib │ │ │ │ ├── GLYCAM_aminoct_06j_10.lib │ │ │ │ ├── GLYCAM_aminont_06j_10.lib │ │ │ │ ├── all_amino02.lib │ │ │ │ ├── all_amino02.r1.lib │ │ │ │ ├── all_amino02EP.lib │ │ │ │ ├── all_amino2011pol.lib │ │ │ │ ├── all_amino91.lib │ │ │ │ ├── all_aminoct02.lib │ │ │ │ ├── all_aminoct02EP.lib │ │ │ │ ├── all_aminoct2011pol.lib │ │ │ │ ├── all_aminoct91.lib │ │ │ │ ├── all_aminont02.lib │ │ │ │ ├── all_aminont02EP.lib │ │ │ │ ├── all_aminont2011pol.lib │ │ │ │ ├── all_aminont91.lib │ │ │ │ ├── all_nucleic02.lib │ │ │ │ ├── all_nucleic02EP.lib │ │ │ │ ├── all_nucleic91.lib │ │ │ │ ├── dna.amberua.lib │ │ │ │ ├── ff02.cmd │ │ │ │ ├── ff02EP.cmd │ │ │ │ ├── ff91.cmd │ │ │ │ ├── ions91.cmd │ │ │ │ ├── ions91.lib │ │ │ │ ├── lipid11.lib │ │ │ │ ├── lipid14.lib │ │ │ │ ├── lipid17.lib │ │ │ │ ├── phosphoaa10.lib │ │ │ │ ├── phosphoaa10.readme │ │ │ │ ├── pro-dna91.nmr.off │ │ │ │ ├── protein.amberua.lib │ │ │ │ └── rna.amberua.lib │ │ │ ├── opc3box.off │ │ │ ├── opc3polbox.off │ │ │ ├── opcbox.off │ │ │ ├── parmBSC0.lib │ │ │ ├── parmBSC1.lib │ │ │ ├── phmd.lib │ │ │ ├── phos_amino94.lib │ │ │ ├── phos_aminofb18.lib │ │ │ ├── phosaa14SB.lib │ │ │ ├── phosaa19SB.lib │ │ │ ├── pol3box.off │ │ │ ├── qspcfwbox.off │ │ │ ├── residues.RNA.parmCHI_YIL.bsc.lib │ │ │ ├── solvents.cmd │ │ │ ├── solvents.lib │ │ │ ├── spcebox.off │ │ │ ├── spcfwbox.off │ │ │ ├── terminal_monophosphate.lib │ │ │ ├── terminalphos.LJbb-RNA.lib │ │ │ ├── tip3pbox.off │ │ │ ├── tip3pfbox.off │ │ │ ├── tip4pbox.off │ │ │ ├── tip4pd.off │ │ │ ├── tip4pewbox.off │ │ │ ├── tip5pbox.off │ │ │ ├── uni_amino03.lib │ │ │ ├── uni_aminoct03.lib │ │ │ ├── uni_aminont03.lib │ │ │ ├── xFPchromophores.lib │ │ │ ├── xFPchromophores.lib.2016 │ │ │ └── xFPchromophores.lib.2022 │ │ │ ├── parm │ │ │ ├── GLYCAM_06EPb.dat │ │ │ ├── GLYCAM_06h.dat │ │ │ ├── GLYCAM_06j.dat │ │ │ ├── all_modrna08.frcmod │ │ │ ├── amberdyes.dat │ │ │ ├── ff-nucleic-OL21.frcmod │ │ │ ├── frcmod.DNA.OL15 │ │ │ ├── frcmod.RNA.LJbb │ │ │ ├── frcmod.ROC-RNA │ │ │ ├── frcmod.ROC-RNA_const │ │ │ ├── frcmod.chcl3 │ │ │ ├── frcmod.chiOL4 │ │ │ ├── frcmod.conste │ │ │ ├── frcmod.constph │ │ │ ├── frcmod.dc4 │ │ │ ├── frcmod.fb15 │ │ │ ├── frcmod.ff02pol.r1 │ │ │ ├── frcmod.ff03 │ │ │ ├── frcmod.ff03ua │ │ │ ├── frcmod.ff12SB │ │ │ ├── frcmod.ff14SB │ │ │ ├── frcmod.ff14SBmodAA │ │ │ ├── frcmod.ff15ipq-19F │ │ │ ├── frcmod.ff15ipq-m │ │ │ ├── frcmod.ff19SB │ │ │ ├── frcmod.ff19SB_XXX │ │ │ ├── frcmod.ff19SBmodAA │ │ │ ├── frcmod.ff99SB │ │ │ ├── frcmod.ff99SB14 │ │ │ ├── frcmod.ff99SBildn │ │ │ ├── frcmod.ff99SBnmr │ │ │ ├── frcmod.ff99SP │ │ │ ├── frcmod.ff99bsc0CG │ │ │ ├── frcmod.ions1lm_1264_spce │ │ │ ├── frcmod.ions1lm_1264_tip3p │ │ │ ├── frcmod.ions1lm_1264_tip4pew │ │ │ ├── frcmod.ions1lm_126_spce │ │ │ ├── frcmod.ions1lm_126_tip3p │ │ │ ├── frcmod.ions1lm_126_tip4pew │ │ │ ├── frcmod.ions1lm_iod │ │ │ ├── frcmod.ions234lm_1264_spce │ │ │ ├── frcmod.ions234lm_1264_tip3p │ │ │ ├── frcmod.ions234lm_1264_tip4pew │ │ │ ├── frcmod.ions234lm_126_spce │ │ │ ├── frcmod.ions234lm_126_tip3p │ │ │ ├── frcmod.ions234lm_126_tip4pew │ │ │ ├── frcmod.ions234lm_hfe_spce │ │ │ ├── frcmod.ions234lm_hfe_tip3p │ │ │ ├── frcmod.ions234lm_hfe_tip4pew │ │ │ ├── frcmod.ions234lm_iod_spce │ │ │ ├── frcmod.ions234lm_iod_tip3p │ │ │ ├── frcmod.ions234lm_iod_tip4pew │ │ │ ├── frcmod.ions_charmm22 │ │ │ ├── frcmod.ionsff99_tip3p │ │ │ ├── frcmod.ionsjc_spce │ │ │ ├── frcmod.ionsjc_tip3p │ │ │ ├── frcmod.ionsjc_tip4pew │ │ │ ├── frcmod.ionslm_1264_fb3 │ │ │ ├── frcmod.ionslm_1264_fb4 │ │ │ ├── frcmod.ionslm_1264_opc │ │ │ ├── frcmod.ionslm_1264_opc3 │ │ │ ├── frcmod.ionslm_126_fb3 │ │ │ ├── frcmod.ionslm_126_fb4 │ │ │ ├── frcmod.ionslm_126_opc │ │ │ ├── frcmod.ionslm_126_opc3 │ │ │ ├── frcmod.ionslm_hfe_fb3 │ │ │ ├── frcmod.ionslm_hfe_fb4 │ │ │ ├── frcmod.ionslm_hfe_opc │ │ │ ├── frcmod.ionslm_hfe_opc3 │ │ │ ├── frcmod.ionslm_iod_fb3 │ │ │ ├── frcmod.ionslm_iod_fb4 │ │ │ ├── frcmod.ionslm_iod_opc │ │ │ ├── frcmod.ionslm_iod_opc3 │ │ │ ├── frcmod.meoh │ │ │ ├── frcmod.nma │ │ │ ├── frcmod.opc │ │ │ ├── frcmod.opc3 │ │ │ ├── frcmod.opc3pol │ │ │ ├── frcmod.opc3pol_HMR4fs │ │ │ ├── frcmod.parmCHI_YIL │ │ │ ├── frcmod.parmbsc0 │ │ │ ├── frcmod.parmbsc0_ezOL1 │ │ │ ├── frcmod.parmbsc1 │ │ │ ├── frcmod.phmd │ │ │ ├── frcmod.phosaa10 │ │ │ ├── frcmod.phosaa14SB │ │ │ ├── frcmod.phosaa19SB │ │ │ ├── frcmod.phosfb18 │ │ │ ├── frcmod.pol3 │ │ │ ├── frcmod.protonated_nucleic │ │ │ ├── frcmod.qspcfw │ │ │ ├── frcmod.shaw │ │ │ ├── frcmod.spce │ │ │ ├── frcmod.spceb │ │ │ ├── frcmod.spcfw │ │ │ ├── frcmod.tip3p │ │ │ ├── frcmod.tip3pf │ │ │ ├── frcmod.tip3pfb │ │ │ ├── frcmod.tip4p │ │ │ ├── frcmod.tip4pd │ │ │ ├── frcmod.tip4pd-a99SB-disp │ │ │ ├── frcmod.tip4pew │ │ │ ├── frcmod.tip4pfb │ │ │ ├── frcmod.tip5p │ │ │ ├── frcmod.urea │ │ │ ├── frcmod.vdWall │ │ │ ├── frcmod.xFPchromophores │ │ │ ├── frcmod.xFPchromophores.2016 │ │ │ ├── frcmod.xFPchromophores.2022 │ │ │ ├── gaff.dat │ │ │ ├── gaff2.dat │ │ │ ├── gaff211.dat │ │ │ ├── lipid11.dat │ │ │ ├── lipid14.dat │ │ │ ├── lipid17.dat │ │ │ ├── lipid21.dat │ │ │ ├── lj_1264_pol.dat │ │ │ ├── music.dat │ │ │ ├── nucgen.dat │ │ │ ├── opls.info │ │ │ ├── opls_parm.dat │ │ │ ├── parm10.dat │ │ │ ├── parm14ipq.dat │ │ │ ├── parm15ipq_10.3.dat │ │ │ ├── parm19.dat │ │ │ ├── parm19ipq.dat │ │ │ ├── parm91.dat │ │ │ ├── parm91X.dat │ │ │ ├── parm91X.ua.dat │ │ │ ├── parm94.dat │ │ │ ├── parm96.dat │ │ │ ├── parm98.dat │ │ │ ├── parm99.dat │ │ │ ├── parm99EP.dat │ │ │ ├── parmAM1.dat │ │ │ ├── parmPM3.dat │ │ │ ├── toyrna.dat │ │ │ └── validate_torsions.py │ │ │ └── prep │ │ │ ├── GLYCAM_06EPb.prep │ │ │ ├── GLYCAM_06j-1.prep │ │ │ ├── GLYCAM_lipids_06h.prep │ │ │ ├── all_amino03.in │ │ │ ├── all_aminoct03.in │ │ │ ├── all_aminont03.in │ │ │ ├── amino10.in │ │ │ ├── amino12.in │ │ │ ├── aminoct10.in │ │ │ ├── aminoct12.in │ │ │ ├── aminont10.in │ │ │ ├── aminont12.in │ │ │ ├── chcl3.in │ │ │ ├── dna_nuc94-bsc0_chiOl4-ezOL1.in │ │ │ ├── epACE.prepin │ │ │ ├── epALA.prepin │ │ │ ├── epARG.prepin │ │ │ ├── epASN.prepin │ │ │ ├── epASP.prepin │ │ │ ├── epCYS.prepin │ │ │ ├── epGLN.prepin │ │ │ ├── epGLU.prepin │ │ │ ├── epGLY.prepin │ │ │ ├── epHID.prepin │ │ │ ├── epHIE.prepin │ │ │ ├── epILE.prepin │ │ │ ├── epLEU.prepin │ │ │ ├── epLYS.prepin │ │ │ ├── epMET.prepin │ │ │ ├── epNME.prepin │ │ │ ├── epPHE.prepin │ │ │ ├── epSER.prepin │ │ │ ├── epTHR.prepin │ │ │ ├── epTRP.prepin │ │ │ ├── epTYR.prepin │ │ │ ├── epVAL.prepin │ │ │ ├── meoh.in │ │ │ ├── nma.in │ │ │ ├── nucleic10.in │ │ │ ├── oldff │ │ │ ├── GLYCAM_06h.prep │ │ │ ├── GLYCAM_06j.prep │ │ │ ├── all.in │ │ │ ├── all_amino02.in │ │ │ ├── all_amino02.r1.in │ │ │ ├── all_amino02EP.in │ │ │ ├── all_amino94.in │ │ │ ├── all_aminoct02.in │ │ │ ├── all_aminoct02EP.in │ │ │ ├── all_aminoct94.in │ │ │ ├── all_aminont02.in │ │ │ ├── all_aminont02EP.in │ │ │ ├── all_aminont94.in │ │ │ ├── all_nuc02.in │ │ │ ├── all_nuc02EP.in │ │ │ ├── all_nuc94.in │ │ │ ├── allct.in │ │ │ ├── allnt.in │ │ │ ├── na.amberua.in │ │ │ ├── opls_nacl.in │ │ │ ├── opls_uni.in │ │ │ ├── opls_unict.in │ │ │ ├── opls_unint.in │ │ │ ├── protein.amberua.C.in │ │ │ ├── protein.amberua.N.in │ │ │ ├── protein.amberua.in │ │ │ ├── uni.in │ │ │ ├── unict.in │ │ │ └── unint.in │ │ │ ├── protonated_nucleic │ │ │ ├── DA+.pdb │ │ │ ├── DA+_noP.pdb │ │ │ ├── DC+.pdb │ │ │ ├── DC+_noP.pdb │ │ │ ├── DG-.pdb │ │ │ ├── DG-_noP.pdb │ │ │ ├── DGE.pdb │ │ │ ├── DGE_noP.pdb │ │ │ ├── DT-.pdb │ │ │ ├── DT-_noP.pdb │ │ │ ├── DTE.pdb │ │ │ ├── DTE_noP.pdb │ │ │ ├── RA+.pdb │ │ │ ├── RA+_noP.pdb │ │ │ ├── RC+.pdb │ │ │ ├── RC+_noP.pdb │ │ │ ├── RG-.pdb │ │ │ ├── RG-_noP.pdb │ │ │ ├── RGE.pdb │ │ │ ├── RGE_noP.pdb │ │ │ ├── RU-.pdb │ │ │ ├── RU-_noP.pdb │ │ │ ├── RUE.pdb │ │ │ └── RUE_noP.pdb │ │ │ ├── toyrna.in │ │ │ ├── uni_amino03.in │ │ │ ├── uni_aminoct03.in │ │ │ └── uni_aminont03.in │ └── lib │ │ ├── libcifparse.so │ │ ├── libcrypto.so.3 │ │ ├── libdf.so.0 │ │ ├── libdf.so.0.0.0 │ │ ├── libhdf5.so.310 │ │ ├── libhdf5.so.310.2.0 │ │ ├── libhdf5_hl.so.310 │ │ ├── libhdf5_hl.so.310.0.2 │ │ ├── libmfhdf.so.0 │ │ ├── libmfhdf.so.0.0.0 │ │ ├── libnetcdf.so.19 │ │ ├── libsff_fortran.so │ │ ├── libsz.so.2 │ │ ├── libsz.so.2.0.1 │ │ ├── libzip.so.5 │ │ └── libzip.so.5.5 ├── amber_macos │ ├── GNU_LGPL_v3 │ ├── LICENSE │ ├── amber.sh │ ├── bin │ │ ├── am1bcc │ │ ├── antechamber │ │ ├── atomtype │ │ ├── bondtype │ │ ├── charmmgen │ │ ├── parmchk2 │ │ ├── sqm │ │ ├── teLeap │ │ ├── tleap │ │ └── wrapped_progs │ │ │ ├── am1bcc │ │ │ ├── antechamber │ │ │ ├── atomtype │ │ │ ├── bondtype │ │ │ └── parmchk2 │ ├── dat │ │ ├── antechamber │ │ │ ├── APS.DAT │ │ │ ├── ATCOR.DAT │ │ │ ├── ATOMTYPE_AMBER.DEF │ │ │ ├── ATOMTYPE_BCC.DEF │ │ │ ├── ATOMTYPE_CHECK.TAB │ │ │ ├── ATOMTYPE_GAS.DEF │ │ │ ├── ATOMTYPE_GFF.DEF │ │ │ ├── ATOMTYPE_GFF2.DEF │ │ │ ├── ATOMTYPE_SYBYL.DEF │ │ │ ├── ATOM_EQU.TYPE │ │ │ ├── BCCPARM.DAT │ │ │ ├── BONDTYPE_CHECK.TAB │ │ │ ├── CONNECT.TPL │ │ │ ├── CORR_NAME_TYPE.DAT │ │ │ ├── ESPPARM.DAT │ │ │ ├── GASPARM.DAT │ │ │ ├── PARMCHK.DAT │ │ │ ├── PARM_BLBA_GAFF.DAT │ │ │ ├── PARM_BLBA_GAFF2.DAT │ │ │ ├── RADIUS.DAT │ │ │ ├── database_sample.def │ │ │ ├── mainchain_sample.dat │ │ │ ├── residuegen_sample.dat │ │ │ └── respgen_addfile_sample.dat │ │ ├── chamber │ │ │ ├── par_all22_prot.inp │ │ │ ├── par_all22_sugar.inp │ │ │ ├── par_all27_prot_na.prm │ │ │ ├── par_all36_carb.prm │ │ │ ├── par_all36_prot.prm │ │ │ ├── top_all22_prot.inp │ │ │ ├── top_all22_sugar.inp │ │ │ ├── top_all27_prot_na.rtf │ │ │ ├── top_all36_carb.rtf │ │ │ ├── top_all36_prot.rtf │ │ │ └── toppar_water_ions.str │ │ └── leap │ │ │ ├── cmd │ │ │ ├── leaprc.DNA.OL15 │ │ │ ├── leaprc.DNA.OL21 │ │ │ ├── leaprc.DNA.bsc1 │ │ │ ├── leaprc.GLYCAM_06EPb │ │ │ ├── leaprc.GLYCAM_06j-1 │ │ │ ├── leaprc.RNA.LJbb │ │ │ ├── leaprc.RNA.OL3 │ │ │ ├── leaprc.RNA.ROC │ │ │ ├── leaprc.RNA.Shaw │ │ │ ├── leaprc.RNA.YIL │ │ │ ├── leaprc.amberdyes │ │ │ ├── leaprc.conste │ │ │ ├── leaprc.constph │ │ │ ├── leaprc.ffAM1 │ │ │ ├── leaprc.ffPM3 │ │ │ ├── leaprc.fluorine.ff15ipq │ │ │ ├── leaprc.gaff │ │ │ ├── leaprc.gaff2 │ │ │ ├── leaprc.lipid21 │ │ │ ├── leaprc.mimetic.ff15ipq │ │ │ ├── leaprc.modrna08 │ │ │ ├── leaprc.music │ │ │ ├── leaprc.phosaa10 │ │ │ ├── leaprc.phosaa14SB │ │ │ ├── leaprc.phosaa19SB │ │ │ ├── leaprc.phosfb18 │ │ │ ├── leaprc.protein.fb15 │ │ │ ├── leaprc.protein.ff03.r1 │ │ │ ├── leaprc.protein.ff03ua │ │ │ ├── leaprc.protein.ff14SB │ │ │ ├── leaprc.protein.ff14SB_modAA │ │ │ ├── leaprc.protein.ff14SBonlysc │ │ │ ├── leaprc.protein.ff15ipq │ │ │ ├── leaprc.protein.ff15ipq-vac │ │ │ ├── leaprc.protein.ff19SB │ │ │ ├── leaprc.protein.ff19SB_modAA │ │ │ ├── leaprc.protein.ff19ipq │ │ │ ├── leaprc.water.fb3 │ │ │ ├── leaprc.water.fb3mod │ │ │ ├── leaprc.water.fb4 │ │ │ ├── leaprc.water.opc │ │ │ ├── leaprc.water.opc3 │ │ │ ├── leaprc.water.opc3pol │ │ │ ├── leaprc.water.spce │ │ │ ├── leaprc.water.spceb │ │ │ ├── leaprc.water.tip3p │ │ │ ├── leaprc.water.tip4pd │ │ │ ├── leaprc.water.tip4pd-a99SBdisp │ │ │ ├── leaprc.water.tip4pew │ │ │ ├── leaprc.xFPchromophores │ │ │ └── oldff │ │ │ │ ├── leaprc.DNA.bsc0 │ │ │ │ ├── leaprc.GLYCAM_04 │ │ │ │ ├── leaprc.GLYCAM_06 │ │ │ │ ├── leaprc.GLYCAM_06EP │ │ │ │ ├── leaprc.GLYCAM_06h │ │ │ │ ├── leaprc.GLYCAM_06h-1 │ │ │ │ ├── leaprc.GLYCAM_06h-12SB │ │ │ │ ├── leaprc.GLYCAM_06j_10 │ │ │ │ ├── leaprc.ff02 │ │ │ │ ├── leaprc.ff02pol.r0 │ │ │ │ ├── leaprc.ff02pol.r1 │ │ │ │ ├── leaprc.ff02polEP.r0 │ │ │ │ ├── leaprc.ff02polEP.r1 │ │ │ │ ├── leaprc.ff03 │ │ │ │ ├── leaprc.ff10 │ │ │ │ ├── leaprc.ff14SB │ │ │ │ ├── leaprc.ff14SB.redq │ │ │ │ ├── leaprc.ff14ipq │ │ │ │ ├── leaprc.ff84 │ │ │ │ ├── leaprc.ff86 │ │ │ │ ├── leaprc.ff94 │ │ │ │ ├── leaprc.ff94.nmr │ │ │ │ ├── leaprc.ff96 │ │ │ │ ├── leaprc.ff98 │ │ │ │ ├── leaprc.ff99 │ │ │ │ ├── leaprc.ff99SB │ │ │ │ ├── leaprc.ff99SBildn │ │ │ │ ├── leaprc.ff99SBnmr │ │ │ │ ├── leaprc.ff99bsc0 │ │ │ │ ├── leaprc.lipid11 │ │ │ │ ├── leaprc.lipid14 │ │ │ │ ├── leaprc.lipid17 │ │ │ │ ├── leaprc.parmbsc0_chiOL4_ezOL1 │ │ │ │ ├── leaprc.rna.ff02 │ │ │ │ ├── leaprc.rna.ff02EP │ │ │ │ ├── leaprc.rna.ff84 │ │ │ │ ├── leaprc.rna.ff94 │ │ │ │ ├── leaprc.rna.ff98 │ │ │ │ ├── leaprc.rna.ff99 │ │ │ │ └── leaprc.toyrna │ │ │ ├── lib │ │ │ ├── 8Murea.readme │ │ │ ├── 8Mureabox.off │ │ │ ├── DNA.OL15.lib │ │ │ ├── DNA_CI.lib │ │ │ ├── GLYCAM_amino_06j_12SB.lib │ │ │ ├── GLYCAM_aminoct_06j_12SB.lib │ │ │ ├── GLYCAM_aminont_06j_12SB.lib │ │ │ ├── Makefile │ │ │ ├── RNA.YIL.lib │ │ │ ├── RNA.lib │ │ │ ├── RNA_CI.lib │ │ │ ├── RNA_Shaw.lib │ │ │ ├── all_amino03.lib │ │ │ ├── all_amino94.lib │ │ │ ├── all_amino94.nmr.lib │ │ │ ├── all_amino94ildn.lib │ │ │ ├── all_aminoAM1.lib │ │ │ ├── all_aminoPM3.lib │ │ │ ├── all_aminoct03.lib │ │ │ ├── all_aminoct94.lib │ │ │ ├── all_aminoct94ildn.lib │ │ │ ├── all_aminoctfb15.lib │ │ │ ├── all_aminofb15.lib │ │ │ ├── all_aminont03.lib │ │ │ ├── all_aminont94.lib │ │ │ ├── all_aminont94ildn.lib │ │ │ ├── all_aminontfb15.lib │ │ │ ├── all_modrna08.lib │ │ │ ├── all_nucleic94.lib │ │ │ ├── all_nucleic94.nmr.lib │ │ │ ├── all_prot_nucleic10.cmd │ │ │ ├── all_prot_nucleic10.lib │ │ │ ├── amberdyes.lib │ │ │ ├── amino10.lib │ │ │ ├── amino12.lib │ │ │ ├── amino12.redq.lib │ │ │ ├── amino14ipq.lib │ │ │ ├── amino15ipq-vac_10.0.lib │ │ │ ├── amino15ipq_10.0.lib │ │ │ ├── amino19.lib │ │ │ ├── amino19ipq_0.9.lib │ │ │ ├── amino19ipq_0.9_pol.lib │ │ │ ├── amino19ipq_0.9_vac.lib │ │ │ ├── aminocn15ipq_10.0.lib │ │ │ ├── aminoct10.lib │ │ │ ├── aminoct12.lib │ │ │ ├── aminoct12.redq.lib │ │ │ ├── aminoct14ipq.lib │ │ │ ├── aminoct15ipq-vac_10.0.lib │ │ │ ├── aminoct15ipq_10.0.lib │ │ │ ├── aminoct19ipq_0.9.lib │ │ │ ├── aminoct19ipq_0.9_pol.lib │ │ │ ├── aminoct19ipq_0.9_vac.lib │ │ │ ├── aminont10.lib │ │ │ ├── aminont12.lib │ │ │ ├── aminont12.redq.lib │ │ │ ├── aminont14ipq.lib │ │ │ ├── aminont15ipq-vac_10.0.lib │ │ │ ├── aminont15ipq_10.0.lib │ │ │ ├── aminont19ipq_0.9.lib │ │ │ ├── aminont19ipq_0.9_pol.lib │ │ │ ├── aminont19ipq_0.9_vac.lib │ │ │ ├── atomic_ions.cmd │ │ │ ├── atomic_ions.lib │ │ │ ├── chcl3box.off │ │ │ ├── conste.lib │ │ │ ├── constph.lib │ │ │ ├── cph_nucleic_caps.lib │ │ │ ├── fb3box.off │ │ │ ├── fb4box.off │ │ │ ├── ff-nucleic-OL21.lib │ │ │ ├── ff03.cmd │ │ │ ├── ff03ua.cmd │ │ │ ├── ff10.cmd │ │ │ ├── ff12SB.cmd │ │ │ ├── ff15ipq-19F.lib │ │ │ ├── ff15ipq-m.lib │ │ │ ├── ff94.cmd │ │ │ ├── ions94.cmd │ │ │ ├── ions94.lib │ │ │ ├── lipid21.lib │ │ │ ├── meohbox.off │ │ │ ├── mk_nablib.cmd │ │ │ ├── mod_amino.lib │ │ │ ├── mod_amino19.lib │ │ │ ├── music.lib │ │ │ ├── nab.lib │ │ │ ├── nmabox.off │ │ │ ├── nucleic10.lib │ │ │ ├── nucleic12.LJbb-RNA.lib │ │ │ ├── nucleic12.ROC-RNA.lib │ │ │ ├── nucleic12.lib │ │ │ ├── nucleic12.redq.lib │ │ │ ├── oldff │ │ │ │ ├── GLYCAM_amino_06j_10.lib │ │ │ │ ├── GLYCAM_aminoct_06j_10.lib │ │ │ │ ├── GLYCAM_aminont_06j_10.lib │ │ │ │ ├── all_amino02.lib │ │ │ │ ├── all_amino02.r1.lib │ │ │ │ ├── all_amino02EP.lib │ │ │ │ ├── all_amino2011pol.lib │ │ │ │ ├── all_amino91.lib │ │ │ │ ├── all_aminoct02.lib │ │ │ │ ├── all_aminoct02EP.lib │ │ │ │ ├── all_aminoct2011pol.lib │ │ │ │ ├── all_aminoct91.lib │ │ │ │ ├── all_aminont02.lib │ │ │ │ ├── all_aminont02EP.lib │ │ │ │ ├── all_aminont2011pol.lib │ │ │ │ ├── all_aminont91.lib │ │ │ │ ├── all_nucleic02.lib │ │ │ │ ├── all_nucleic02EP.lib │ │ │ │ ├── all_nucleic91.lib │ │ │ │ ├── dna.amberua.lib │ │ │ │ ├── ff02.cmd │ │ │ │ ├── ff02EP.cmd │ │ │ │ ├── ff91.cmd │ │ │ │ ├── ions91.cmd │ │ │ │ ├── ions91.lib │ │ │ │ ├── lipid11.lib │ │ │ │ ├── lipid14.lib │ │ │ │ ├── lipid17.lib │ │ │ │ ├── phosphoaa10.lib │ │ │ │ ├── phosphoaa10.readme │ │ │ │ ├── pro-dna91.nmr.off │ │ │ │ ├── protein.amberua.lib │ │ │ │ └── rna.amberua.lib │ │ │ ├── opc3box.off │ │ │ ├── opc3polbox.off │ │ │ ├── opcbox.off │ │ │ ├── parmBSC0.lib │ │ │ ├── parmBSC1.lib │ │ │ ├── phmd.lib │ │ │ ├── phos_amino94.lib │ │ │ ├── phos_aminofb18.lib │ │ │ ├── phosaa14SB.lib │ │ │ ├── phosaa19SB.lib │ │ │ ├── pol3box.off │ │ │ ├── qspcfwbox.off │ │ │ ├── residues.RNA.parmCHI_YIL.bsc.lib │ │ │ ├── solvents.cmd │ │ │ ├── solvents.lib │ │ │ ├── spcebox.off │ │ │ ├── spcfwbox.off │ │ │ ├── terminal_monophosphate.lib │ │ │ ├── terminalphos.LJbb-RNA.lib │ │ │ ├── tip3pbox.off │ │ │ ├── tip3pfbox.off │ │ │ ├── tip4pbox.off │ │ │ ├── tip4pd.off │ │ │ ├── tip4pewbox.off │ │ │ ├── tip5pbox.off │ │ │ ├── uni_amino03.lib │ │ │ ├── uni_aminoct03.lib │ │ │ ├── uni_aminont03.lib │ │ │ ├── xFPchromophores.lib │ │ │ ├── xFPchromophores.lib.2016 │ │ │ └── xFPchromophores.lib.2022 │ │ │ ├── parm │ │ │ ├── GLYCAM_06EPb.dat │ │ │ ├── GLYCAM_06h.dat │ │ │ ├── GLYCAM_06j.dat │ │ │ ├── all_modrna08.frcmod │ │ │ ├── amberdyes.dat │ │ │ ├── ff-nucleic-OL21.frcmod │ │ │ ├── frcmod.DNA.OL15 │ │ │ ├── frcmod.RNA.LJbb │ │ │ ├── frcmod.ROC-RNA │ │ │ ├── frcmod.ROC-RNA_const │ │ │ ├── frcmod.chcl3 │ │ │ ├── frcmod.chiOL4 │ │ │ ├── frcmod.conste │ │ │ ├── frcmod.constph │ │ │ ├── frcmod.dc4 │ │ │ ├── frcmod.fb15 │ │ │ ├── frcmod.ff02pol.r1 │ │ │ ├── frcmod.ff03 │ │ │ ├── frcmod.ff03ua │ │ │ ├── frcmod.ff12SB │ │ │ ├── frcmod.ff14SB │ │ │ ├── frcmod.ff14SBmodAA │ │ │ ├── frcmod.ff15ipq-19F │ │ │ ├── frcmod.ff15ipq-m │ │ │ ├── frcmod.ff19SB │ │ │ ├── frcmod.ff19SB_XXX │ │ │ ├── frcmod.ff19SBmodAA │ │ │ ├── frcmod.ff99SB │ │ │ ├── frcmod.ff99SB14 │ │ │ ├── frcmod.ff99SBildn │ │ │ ├── frcmod.ff99SBnmr │ │ │ ├── frcmod.ff99SP │ │ │ ├── frcmod.ff99bsc0CG │ │ │ ├── frcmod.ions1lm_1264_spce │ │ │ ├── frcmod.ions1lm_1264_tip3p │ │ │ ├── frcmod.ions1lm_1264_tip4pew │ │ │ ├── frcmod.ions1lm_126_spce │ │ │ ├── frcmod.ions1lm_126_tip3p │ │ │ ├── frcmod.ions1lm_126_tip4pew │ │ │ ├── frcmod.ions1lm_iod │ │ │ ├── frcmod.ions234lm_1264_spce │ │ │ ├── frcmod.ions234lm_1264_tip3p │ │ │ ├── frcmod.ions234lm_1264_tip4pew │ │ │ ├── frcmod.ions234lm_126_spce │ │ │ ├── frcmod.ions234lm_126_tip3p │ │ │ ├── frcmod.ions234lm_126_tip4pew │ │ │ ├── frcmod.ions234lm_hfe_spce │ │ │ ├── frcmod.ions234lm_hfe_tip3p │ │ │ ├── frcmod.ions234lm_hfe_tip4pew │ │ │ ├── frcmod.ions234lm_iod_spce │ │ │ ├── frcmod.ions234lm_iod_tip3p │ │ │ ├── frcmod.ions234lm_iod_tip4pew │ │ │ ├── frcmod.ions_charmm22 │ │ │ ├── frcmod.ionsff99_tip3p │ │ │ ├── frcmod.ionsjc_spce │ │ │ ├── frcmod.ionsjc_tip3p │ │ │ ├── frcmod.ionsjc_tip4pew │ │ │ ├── frcmod.ionslm_1264_fb3 │ │ │ ├── frcmod.ionslm_1264_fb4 │ │ │ ├── frcmod.ionslm_1264_opc │ │ │ ├── frcmod.ionslm_1264_opc3 │ │ │ ├── frcmod.ionslm_126_fb3 │ │ │ ├── frcmod.ionslm_126_fb4 │ │ │ ├── frcmod.ionslm_126_opc │ │ │ ├── frcmod.ionslm_126_opc3 │ │ │ ├── frcmod.ionslm_hfe_fb3 │ │ │ ├── frcmod.ionslm_hfe_fb4 │ │ │ ├── frcmod.ionslm_hfe_opc │ │ │ ├── frcmod.ionslm_hfe_opc3 │ │ │ ├── frcmod.ionslm_iod_fb3 │ │ │ ├── frcmod.ionslm_iod_fb4 │ │ │ ├── frcmod.ionslm_iod_opc │ │ │ ├── frcmod.ionslm_iod_opc3 │ │ │ ├── frcmod.meoh │ │ │ ├── frcmod.nma │ │ │ ├── frcmod.opc │ │ │ ├── frcmod.opc3 │ │ │ ├── frcmod.opc3pol │ │ │ ├── frcmod.opc3pol_HMR4fs │ │ │ ├── frcmod.parmCHI_YIL │ │ │ ├── frcmod.parmbsc0 │ │ │ ├── frcmod.parmbsc0_ezOL1 │ │ │ ├── frcmod.parmbsc1 │ │ │ ├── frcmod.phmd │ │ │ ├── frcmod.phosaa10 │ │ │ ├── frcmod.phosaa14SB │ │ │ ├── frcmod.phosaa19SB │ │ │ ├── frcmod.phosfb18 │ │ │ ├── frcmod.pol3 │ │ │ ├── frcmod.protonated_nucleic │ │ │ ├── frcmod.qspcfw │ │ │ ├── frcmod.shaw │ │ │ ├── frcmod.spce │ │ │ ├── frcmod.spceb │ │ │ ├── frcmod.spcfw │ │ │ ├── frcmod.tip3p │ │ │ ├── frcmod.tip3pf │ │ │ ├── frcmod.tip3pfb │ │ │ ├── frcmod.tip4p │ │ │ ├── frcmod.tip4pd │ │ │ ├── frcmod.tip4pd-a99SB-disp │ │ │ ├── frcmod.tip4pew │ │ │ ├── frcmod.tip4pfb │ │ │ ├── frcmod.tip5p │ │ │ ├── frcmod.urea │ │ │ ├── frcmod.vdWall │ │ │ ├── frcmod.xFPchromophores │ │ │ ├── frcmod.xFPchromophores.2016 │ │ │ ├── frcmod.xFPchromophores.2022 │ │ │ ├── gaff.dat │ │ │ ├── gaff2.dat │ │ │ ├── gaff211.dat │ │ │ ├── lipid11.dat │ │ │ ├── lipid14.dat │ │ │ ├── lipid17.dat │ │ │ ├── lipid21.dat │ │ │ ├── lj_1264_pol.dat │ │ │ ├── music.dat │ │ │ ├── nucgen.dat │ │ │ ├── opls.info │ │ │ ├── opls_parm.dat │ │ │ ├── parm10.dat │ │ │ ├── parm14ipq.dat │ │ │ ├── parm15ipq_10.3.dat │ │ │ ├── parm19.dat │ │ │ ├── parm19ipq.dat │ │ │ ├── parm91.dat │ │ │ ├── parm91X.dat │ │ │ ├── parm91X.ua.dat │ │ │ ├── parm94.dat │ │ │ ├── parm96.dat │ │ │ ├── parm98.dat │ │ │ ├── parm99.dat │ │ │ ├── parm99EP.dat │ │ │ ├── parmAM1.dat │ │ │ ├── parmPM3.dat │ │ │ ├── toyrna.dat │ │ │ └── validate_torsions.py │ │ │ └── prep │ │ │ ├── GLYCAM_06EPb.prep │ │ │ ├── GLYCAM_06j-1.prep │ │ │ ├── GLYCAM_lipids_06h.prep │ │ │ ├── all_amino03.in │ │ │ ├── all_aminoct03.in │ │ │ ├── all_aminont03.in │ │ │ ├── amino10.in │ │ │ ├── amino12.in │ │ │ ├── aminoct10.in │ │ │ ├── aminoct12.in │ │ │ ├── aminont10.in │ │ │ ├── aminont12.in │ │ │ ├── chcl3.in │ │ │ ├── dna_nuc94-bsc0_chiOl4-ezOL1.in │ │ │ ├── epACE.prepin │ │ │ ├── epALA.prepin │ │ │ ├── epARG.prepin │ │ │ ├── epASN.prepin │ │ │ ├── epASP.prepin │ │ │ ├── epCYS.prepin │ │ │ ├── epGLN.prepin │ │ │ ├── epGLU.prepin │ │ │ ├── epGLY.prepin │ │ │ ├── epHID.prepin │ │ │ ├── epHIE.prepin │ │ │ ├── epILE.prepin │ │ │ ├── epLEU.prepin │ │ │ ├── epLYS.prepin │ │ │ ├── epMET.prepin │ │ │ ├── epNME.prepin │ │ │ ├── epPHE.prepin │ │ │ ├── epSER.prepin │ │ │ ├── epTHR.prepin │ │ │ ├── epTRP.prepin │ │ │ ├── epTYR.prepin │ │ │ ├── epVAL.prepin │ │ │ ├── meoh.in │ │ │ ├── nma.in │ │ │ ├── nucleic10.in │ │ │ ├── oldff │ │ │ ├── GLYCAM_06h.prep │ │ │ ├── GLYCAM_06j.prep │ │ │ ├── all.in │ │ │ ├── all_amino02.in │ │ │ ├── all_amino02.r1.in │ │ │ ├── all_amino02EP.in │ │ │ ├── all_amino94.in │ │ │ ├── all_aminoct02.in │ │ │ ├── all_aminoct02EP.in │ │ │ ├── all_aminoct94.in │ │ │ ├── all_aminont02.in │ │ │ ├── all_aminont02EP.in │ │ │ ├── all_aminont94.in │ │ │ ├── all_nuc02.in │ │ │ ├── all_nuc02EP.in │ │ │ ├── all_nuc94.in │ │ │ ├── allct.in │ │ │ ├── allnt.in │ │ │ ├── na.amberua.in │ │ │ ├── opls_nacl.in │ │ │ ├── opls_uni.in │ │ │ ├── opls_unict.in │ │ │ ├── opls_unint.in │ │ │ ├── protein.amberua.C.in │ │ │ ├── protein.amberua.N.in │ │ │ ├── protein.amberua.in │ │ │ ├── uni.in │ │ │ ├── unict.in │ │ │ └── unint.in │ │ │ ├── protonated_nucleic │ │ │ ├── DA+.pdb │ │ │ ├── DA+_noP.pdb │ │ │ ├── DC+.pdb │ │ │ ├── DC+_noP.pdb │ │ │ ├── DG-.pdb │ │ │ ├── DG-_noP.pdb │ │ │ ├── DGE.pdb │ │ │ ├── DGE_noP.pdb │ │ │ ├── DT-.pdb │ │ │ ├── DT-_noP.pdb │ │ │ ├── DTE.pdb │ │ │ ├── DTE_noP.pdb │ │ │ ├── RA+.pdb │ │ │ ├── RA+_noP.pdb │ │ │ ├── RC+.pdb │ │ │ ├── RC+_noP.pdb │ │ │ ├── RG-.pdb │ │ │ ├── RG-_noP.pdb │ │ │ ├── RGE.pdb │ │ │ ├── RGE_noP.pdb │ │ │ ├── RU-.pdb │ │ │ ├── RU-_noP.pdb │ │ │ ├── RUE.pdb │ │ │ └── RUE_noP.pdb │ │ │ ├── toyrna.in │ │ │ ├── uni_amino03.in │ │ │ ├── uni_aminoct03.in │ │ │ └── uni_aminont03.in │ └── lib │ │ ├── libarpack.2.1.0.dylib │ │ ├── libarpack.2.dylib │ │ ├── libblas.3.dylib │ │ ├── libblosc.1.21.5.dylib │ │ ├── libblosc.1.dylib │ │ ├── libcifparse.dylib │ │ ├── libcrypto.3.dylib │ │ ├── libdf.0.dylib │ │ ├── libdf.dylib │ │ ├── libgcc_s.1.1.dylib │ │ ├── libgfortran.5.dylib │ │ ├── libhdf5.310.dylib │ │ ├── libhdf5.dylib │ │ ├── libhdf5_hl.310.dylib │ │ ├── libhdf5_hl.dylib │ │ ├── libjpeg.8.3.2.dylib │ │ ├── libjpeg.8.dylib │ │ ├── liblapack.3.dylib │ │ ├── liblz4.1.9.4.dylib │ │ ├── liblz4.1.dylib │ │ ├── libmfhdf.0.dylib │ │ ├── libmfhdf.dylib │ │ ├── libnetcdf.19.dylib │ │ ├── libomp.dylib │ │ ├── libopenblas.0.dylib │ │ ├── libquadmath.0.dylib │ │ ├── libsff_fortran.dylib │ │ ├── libsnappy.1.1.10.dylib │ │ ├── libsnappy.1.dylib │ │ ├── libsz.2.0.1.dylib │ │ ├── libsz.2.dylib │ │ ├── libzip.5.5.dylib │ │ ├── libzip.5.dylib │ │ ├── libzstd.1.5.5.dylib │ │ └── libzstd.1.dylib ├── cli.py ├── logger.py ├── mol.py ├── params.py ├── parser_args.py ├── topol.py └── utils.py ├── acpype_docker.bat ├── acpype_docker.sh ├── charmmgen_linux.tgz ├── charmmgen_macos.tgz ├── docs ├── Makefile ├── _templates │ ├── custom-class-template.rst │ └── custom-module-template.rst ├── conf.py ├── index.rst ├── make.bat └── requirements.txt ├── ffamber_additions ├── FF.dat ├── README.txt ├── ions.itp ├── parm10gaff.dat ├── parm99SBgaff.dat ├── parm99bsc0SBgaff.dat ├── spc.itp ├── spce.itp └── tip3p.itp ├── legacy └── CcpnToAcpype.py ├── poetry.lock ├── pyproject.toml ├── recipe ├── build.sh ├── meta.yaml └── setup_conda.py ├── release.sh ├── run_acpype.py ├── scripts ├── Data │ ├── 1BVG.pdb │ ├── ComplexAmber_GMX.gro │ ├── ComplexAmber_GMX.top │ ├── Ligand.itp │ └── res_acpype_x_gmx_comparison_pymol.txt ├── acpype_ligands_results.txt ├── ambXgmxEner.py ├── analyse_test_acpype_db_ligands.py ├── check_acpype.py ├── compare_itps.py ├── run_test_acpype_db_ligands.py ├── script_test.sh └── ver_today.sh ├── tests ├── AAA.mol2 ├── AAA.pdb ├── ADPMg.mol2 ├── Base.inpcrd ├── Base.prmtop ├── ComplexG1.inpcrd ├── ComplexG1.prmtop ├── ComplexG2.inpcrd ├── ComplexG2.prmtop ├── DDD.pdb ├── DNA_BSC0.inpcrd ├── DNA_BSC0.prmtop ├── FFF.mol2 ├── FFF.pdb ├── HEM.mol2 ├── HEM.pdb ├── ILDN.inpcrd ├── ILDN.prmtop ├── KKK.mol2 ├── KKK.pdb ├── RAMP1_ion.inpcrd ├── RAMP1_ion.prmtop ├── README.txt ├── __init__.py ├── benzene.mdl ├── benzene.mol ├── benzene.pdb ├── conftest.py ├── dmp.mol2 ├── dmp.pdb ├── double_res.pdb ├── drift.mol2 ├── em.mdp ├── glycam_corrupt.prmtop ├── glycam_empty.inpcrd ├── glycam_empty.prmtop ├── glycam_exe.inpcrd ├── glycam_exe.prmtop ├── lower_res.pdb ├── md.mdp ├── no_res.pdb ├── same_coord.pdb ├── test_acpype.py ├── test_acs_api.py ├── test_amb2gmx.py ├── test_mol.py ├── test_scenarios.py ├── thalidomide.mol2 ├── too_close.pdb ├── too_far.pdb ├── wrong_res_num.pdb ├── wrong_res_set.pdb └── wrong_res_sym.pdb ├── tox.ini ├── update_linux_bins.sh └── update_macos_bins.sh /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/alanwilter/acpype/HEAD/.gitattributes -------------------------------------------------------------------------------- /.github/workflows/check_acpype.yml: -------------------------------------------------------------------------------- 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