├── .gitignore ├── LICENSE ├── README.md ├── crd ├── 0README └── expl_sphere.crd ├── dock ├── dock_ligand.inp ├── enzydock.inp ├── enzydock_main.inp ├── gbsw_cluster.inp ├── ligand_mk_conformers.inp ├── ligand_simulate.inp ├── match_seed_vac.inp ├── mm.inp ├── mm_cluster.inp ├── pbeq_cluster.inp ├── qmmm.inp ├── qmmm_cluster.inp ├── renew_qmmm.inp ├── renew_qmmm_main.inp └── rmsd_dock.inp ├── local_top ├── covalent.str ├── covalent.str_bck ├── grid_probes.prm ├── grid_probes.rtf ├── par_all36_cgenff.prm ├── par_all36_prot.prm ├── top_all36_cgenff.rtf ├── top_all36_prot.rtf └── toppar_water_ions.str ├── pdb └── 0README ├── psf └── 0README ├── results └── 0README ├── scr └── 0README ├── scripts ├── __pycache__ │ ├── calc_rmsd_perm.cpython-36.pyc │ ├── read_write_pdb.cpython-36.pyc │ └── temp ├── calc_rmsd_perm.py ├── cluster_ligands.py ├── cluster_ligands_perm.py ├── cluster_water.py ├── code_update_v1.0g6.csh ├── define_system_var.csh ├── files_lock.csh ├── files_lock.sh ├── get_qm_atom_type.py ├── lp.py ├── mcs_align_match.py ├── mk_report.py ├── pdb_reader.py ├── prepare.py ├── proc_noes.py ├── python_wrapper.sh ├── read_write_pdb.py ├── ring_aromatic.py ├── setup_enzydock_.csh ├── smiles_tors.py ├── softlink.py ├── superpose_cluster_ligands.py ├── tmp │ ├── cluster_ligands.py.bck │ ├── lig_1_7kyu_hf3c0_1_1.pdb │ ├── read_write_pdb.py.bck │ ├── smiles_tors.py.bck │ ├── smiles_tors.py.bck2 │ ├── temp │ └── write_qchem_inp.py_orig └── write_qchem_inp.py ├── stream ├── back_clear_restraints.str ├── back_flex.str ├── back_flex_ng.str ├── check_natoms.str ├── clear_all_restraints.str ├── clear_restraints.str ├── cofact_patch_offgrid.str ├── cofact_patch_ongrid.str ├── consdef │ ├── consensus_def.str │ ├── fp_def.str │ └── userrestraints.str ├── consensus_docking.str ├── cov_generate_offgrid.str ├── cov_generate_ongrid.str ├── cov_ligcofac.str ├── cov_mov_lig.str ├── define_flex_offgrid.str ├── define_flex_ongrid.str ├── define_halfcof.str ├── delete_flex.str ├── disulf.str ├── expl_water.str ├── fp_docking.str ├── gbsw │ ├── radius_gbsw.str │ └── radius_gbsw.str.orig ├── generate_cofactors.str ├── generate_grid.str ├── generate_protein.str ├── mc │ ├── mc_add.str │ ├── mc_delete.str │ ├── mc_sidechains.str │ └── mc_sidechains_delete.str ├── mc_tors.str ├── mc_trot.str ├── mk_userrestraints.str ├── no_samd.str ├── param.str ├── param_set_check.str ├── patch_offgrid.str ├── patch_ongrid.str ├── patching │ ├── cov_patch_g.str │ ├── cov_patch_ng.str │ └── set_prot_patch.str ├── pbeq │ └── radius_pbeq.str ├── qmmm │ ├── qchem1.inp │ └── qchem2.inp ├── read_flex.str ├── read_grid.str ├── read_ligand.str ├── read_protein.str ├── read_psf_crd_protein.str ├── read_water.str ├── read_water_expl.str ├── read_water_in.str ├── read_water_out.str ├── read_write_protein.str ├── rseed.str ├── samd.str ├── samd_1.str ├── seed.str ├── setup_protein.str ├── softlink.str ├── top_prm_all.str ├── usegbsw.str ├── usepbeq.str ├── useqmmm.str ├── userparam.str ├── write_flex.str └── zero_consensus_docking.str └── tests ├── 3js1 ├── local_top │ └── ligand_1.str ├── pdb │ ├── 3js1_1.pdb │ ├── 3js1_wat.pdb │ └── ligand_1.pdb └── stream │ └── userparam.str ├── README ├── abyu ├── local_top │ ├── ligand_1.str │ ├── ligand_2.str │ └── ligand_3.str ├── pdb │ ├── 5dyv_1.pdb │ ├── ligand_1.pdb │ ├── ligand_2.pdb │ └── ligand_3.pdb └── stream │ ├── consdef │ ├── 2_consensus_data.str │ └── 3_consensus_data.str │ └── userparam.str ├── as ├── crd │ └── 4kwd_withoutligand.crd ├── local_top │ ├── 4kwd_pop.prm │ ├── 4kwd_pop.rtf │ ├── ligand_1.str │ └── ligand_1_pop_patch.str ├── pdb │ ├── 4kwd_1_not_cgui.pdb │ ├── 4kwd_mg.pdb │ ├── 4kwd_pop.pdb │ ├── 4kwd_wat.pdb │ └── ligand_1.pdb ├── psf │ └── 4kwd_withoutligand.psf └── stream │ ├── patching │ └── cofact1_patch_1.str │ └── userparam.str ├── bpps ├── local_top │ ├── 1n23_pop.str │ ├── ligand_1.str │ ├── ligand_2.str │ ├── ligand_3.str │ ├── ligand_4.str │ ├── ligand_4_pop_patch.str │ ├── ligand_5.str │ └── ligand_5_pop_patch.str ├── pdb │ ├── 1n23_1.pdb │ ├── 1n23_cwat.pdb │ ├── 1n23_mg.pdb │ ├── 1n23_pop.pdb │ ├── ligand_1.pdb │ ├── ligand_2.pdb │ ├── ligand_3.pdb │ ├── ligand_4.pdb │ └── ligand_5.pdb └── stream │ ├── consdef │ └── user_consensus.csv │ ├── patching │ ├── cofact1_patch_4.str │ └── cofact1_patch_5.str │ └── userparam.str ├── cotb2 ├── local_top │ ├── cotb2_pop.prm │ ├── cotb2_pop.rtf │ ├── ligand_1.str │ ├── ligand_2.str │ ├── ligand_3.str │ ├── ligand_4.str │ ├── ligand_5.str │ ├── ligand_6.str │ ├── ligand_7.str │ ├── ligand_8.str │ ├── ligand_8_pop_patch.str │ └── ligand_9.str ├── pdb │ ├── cotb2_1.pdb │ ├── cotb2_mg.pdb │ ├── cotb2_pop.pdb │ ├── cotb2_wat.pdb │ ├── ligand_1.pdb │ ├── ligand_2.pdb │ ├── ligand_3.pdb │ ├── ligand_4.pdb │ ├── ligand_5.pdb │ ├── ligand_6.pdb │ ├── ligand_7.pdb │ ├── ligand_8.pdb │ └── ligand_9.pdb └── stream │ ├── patching │ └── cofact1_patch_8.str │ └── userparam.str ├── lepi ├── local_top │ ├── 6j24_sam.prm │ ├── 6j24_sam.rtf │ ├── ligand_1.str │ ├── ligand_2.str │ ├── ligand_3.str │ ├── ligand_4.str │ └── ligand_5.str ├── pdb │ ├── 6j24_1.pdb │ ├── 6j24_2.pdb │ ├── 6j24_sam.pdb │ ├── ligand_0.pdb │ ├── ligand_1.pdb │ ├── ligand_2.pdb │ ├── ligand_3.pdb │ ├── ligand_4.pdb │ └── ligand_5.pdb └── stream │ ├── consdef │ ├── user_consensus.csv │ └── userrestraints.csv │ ├── patching │ ├── patch_g_5.str │ ├── patch_ng_5.str │ └── set_prot_patch.str │ └── userparam.str ├── micha ├── local_top │ └── ligand_1.str ├── pdb │ ├── 2hwo_1.pdb │ └── ligand_1.pdb └── stream │ ├── consdef │ └── userrestraints.str │ └── userparam.str ├── pror ├── local_top │ ├── ligand_1.str │ ├── ligand_2.str │ └── ligand_3.str ├── pdb │ ├── 1w61_1.pdb │ ├── 1w61_2.pdb │ ├── ligand_1.pdb │ ├── ligand_2.pdb │ └── ligand_3.pdb └── stream │ ├── patching │ ├── patch_g_1.str │ ├── patch_g_2.str │ ├── patch_g_3.str │ ├── patch_ng_1.str │ ├── patch_ng_2.str │ ├── patch_ng_3.str │ └── set_prot_patch.str │ └── userparam.str └── serr ├── local_top ├── 3l6b_mn.str ├── 3l6b_plp.str └── 3l6b_plp_patch.str ├── org_lig ├── ligand_1.pdb ├── ligand_1.str ├── ligand_2.pdb ├── ligand_2.str ├── ligand_3.pdb └── ligand_3.str ├── pdb ├── 3l6b.pdb ├── 3l6b_1.pdb ├── 3l6b_mn.pdb ├── 3l6b_plp.pdb └── ligands.csv └── stream ├── patching ├── cofact1_patch_g_1.str ├── cofact1_patch_g_2.str ├── cofact1_patch_g_3.str ├── cofact1_patch_ng_1.str ├── cofact1_patch_ng_2.str └── cofact1_patch_ng_3.str └── userparam.str /.gitignore: -------------------------------------------------------------------------------- 1 | 6y2g_hf3c09.tar.gz 2 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/majordt/EnzyDock/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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