Galaxy | BIOBB | Published Workflow | GMX Protein Ligand Complex MD Setup

GMX Protein Ligand Complex MD Setup

Annotation:

Step	Annotation
Step 1: Pdb output PDB name mypdb_prot.pdb Take tool settings: Manual Input Properties Input: pdb_code 3htb filter Empty. api_id pdbe - PDB in Europe REST API
Step 2: ExtractHeteroatoms input PDB,PDBQT file Output dataset 'output_pdb_path' from step 1 output PDB,PDBQT name myextract_heteroatoms.pdb Take tool settings: Manual Input Properties Input: heteroatoms [{"name": "JZ4"}] water False output_format pdb
Step 3: ExtractMolecule input PDB,PDBQT file Output dataset 'output_pdb_path' from step 1 output PDB,PDBQT name myextract_molecule.pdb Take tool settings: Manual Input Properties Input: molecule_type all chains [] binary_path check_structure output_format pdb
Step 4: ReduceAddHydrogens input PDB file Output dataset 'output_heteroatom_path' from step 2 output PDB name myreduce_add_hydrogens.pdb Take tool settings: Manual Input Properties Input: flip False noflip False nuclear True nooh False oh True his False noheth False rotnh3 True norotnh3 False rotexist False rotexoh False allalt True onlya False charges False dorotmet False noadjust False metal_bump 0.0 non_metal_bump 0.0 build False binary_path reduce
Step 5: FixSideChain input PDB file Output dataset 'output_molecule_path' from step 3 output PDB name myfix_side_chain.pdb Take tool settings: Manual Input Properties Input: use_modeller False modeller_key Not available. binary_path check_structure
Step 6: BabelMinimize input PDB,MOL2 file Output dataset 'output_path' from step 4 output PDB,MOL2 name mybabel_minimize.mol2 Take tool settings: Manual Input Properties Input: criteria 1e-10 method sd - steepest descent algorithm force_field GAFF - General Amber Force Field hydrogens False steps 2500 cutoff False rvdw 6.0 rele 10.0 frequency 10 binary_path obminimize output_format pdb
Step 7: Pdb2gmx input PDB file Output dataset 'output_pdb_path' from step 5 output GRO name mypdb2gmx.gro output ZIP name mypdb2gmx.zip Take tool settings: Manual Input Properties Input: water_type spce force_field amber99sb-ildn ignh False his Not available. merge False gmx_lib Not available. binary_path gmx
Step 8: AcpypeParamsGmx input PDB,MDL,MOL2 file Output dataset 'output_path' from step 6 output GRO name myacpype_params_gmx.gro output ITP name myacpype_params_gmx.itp output TOP name myacpype_params_gmx.top Take tool settings: Manual Input Properties Input: basename JZ4params charge 0 binary_path acpype
Step 9: GmxTrjconvStr input XTC,TRR,CPT,GRO,G96,PDB,TNG file Output dataset 'output_gro_path' from step 7 input TPR,GRO,G96,PDB,BRK,ENT file Output dataset 'output_gro_path' from step 7 input NDX file select at runtime output PDB,XTC,TRR,CPT,GRO,G96,TNG name mygmx_trjconv_str_prot.pdb Take tool settings: Manual Input Properties Input: selection System - all atoms in the system pbc none - No PBC treatment center True ur compact - Puts all atoms at the closest distance from the center of the box fit none binary_path gmx output_format pdb
Step 10: MakeNdx input GRO,PDB,TPR file Output dataset 'output_path_gro' from step 8 input NDX file select at runtime output NDX name mymake_ndx.ndx Take tool settings: Manual Input Properties Input: selection 0 & ! a H* gmx_lib Empty. binary_path gmx
Step 11: GmxTrjconvStr input XTC,TRR,CPT,GRO,G96,PDB,TNG file Output dataset 'output_path_gro' from step 8 input TPR,GRO,G96,PDB,BRK,ENT file Output dataset 'output_path_gro' from step 8 input NDX file select at runtime output PDB,XTC,TRR,CPT,GRO,G96,TNG name mygmx_trjconv_str_lig.pdb Take tool settings: Manual Input Properties Input: selection System - all atoms in the system pbc none - No PBC treatment center True ur compact - Puts all atoms at the closest distance from the center of the box fit none binary_path gmx output_format pdb
Step 12: Genrestr input PDB,GRO,TPR file Output dataset 'output_path_gro' from step 8 input NDX file Output dataset 'output_ndx_path' from step 10 output ITP name mygenrestr.itp Take tool settings: Manual Input Properties Input: restrained_group System force_constants 1000 1000 1000 gmx_lib Empty. binary_path gmx
Step 13: CatPdb input PDB,PDBQT file Output dataset 'output_str_path' from step 9 input PDB,PDBQT file Output dataset 'output_str_path' from step 11 output PDB,PDBQT name mycat_pdb.pdb Take tool settings: Manual Input Properties Input: output_format pdb
Step 14: AppendLigand input ZIP file Output dataset 'output_top_zip_path' from step 7 input ITP file Output dataset 'output_path_itp' from step 8 input ITP file Output dataset 'output_itp_path' from step 12 output ZIP name myappend_ligand.zip Take tool settings: Manual Input Properties Input: posres_name POSRES_JZ4
Step 15: Editconf input GRO,PDB file Output dataset 'output_structure_path' from step 13 output PDB,GRO name myeditconf.gro Take tool settings: Manual Input Properties Input: distance_to_molecule 0.8 box_vector_lenghts Not available. box_type octahedron - truncated octahedron center_molecule True gmx_lib Empty. binary_path gmx output_format pdb
Step 16: Solvate input GRO,PDB file Output dataset 'output_gro_path' from step 15 input ZIP file Output dataset 'output_top_zip_path' from step 14 input GRO file select at runtime output GRO,PDB name mysolvate.gro output ZIP name mysolvate.zip Take tool settings: Manual Input Properties Input: shell 0.0 gmx_lib Empty. binary_path gmx output_format gro
Step 17: Grompp input GRO file Output dataset 'output_gro_path' from step 16 input ZIP file Output dataset 'output_top_zip_path' from step 16 input CPT file select at runtime input NDX file select at runtime input MDP file select at runtime output TPR name mygrompp_ion.tpr Take tool settings: Manual Input Properties Input: mdp {"nsteps": "5000"} simulation_type minimization - Energy minimization using steepest descent algorithm is used maxwarn 1 gmx_lib Empty. binary_path gmx
Step 18: Genion input TPR file Output dataset 'output_tpr_path' from step 17 input ZIP file Output dataset 'output_top_zip_path' from step 16 input NDX file select at runtime output GRO name mygenion.gro output ZIP name mygenion.zip Take tool settings: Manual Input Properties Input: replaced_group SOL neutral True concentration 0.05 seed 1993 gmx_lib Empty. binary_path gmx
Step 19: Grompp input GRO file Output dataset 'output_gro_path' from step 18 input ZIP file Output dataset 'output_top_zip_path' from step 18 input CPT file select at runtime input NDX file select at runtime input MDP file select at runtime output TPR name mygrompp.tpr Take tool settings: Manual Input Properties Input: mdp {"nsteps": "5000", "emstep": 0.01, "emtol": "500"} simulation_type minimization - Energy minimization using steepest descent algorithm is used maxwarn 0 gmx_lib Empty. binary_path gmx
Step 20: Mdrun input TPR file Output dataset 'output_tpr_path' from step 19 input CPT file select at runtime output GRO name mymdrun.gro output EDR name mymdrun.edr output LOG name mymdrun.log output TRR name mymdrun.trr output XTC name mymdrun.xtc output CPT name mymdrun.cpt output XVG name mymdrun.xvg Take tool settings: Manual Input Properties Input: mpi_bin Empty. mpi_np 0 mpi_flags Empty. checkpoint_time 15 num_threads 0 num_threads_mpi 0 num_threads_omp 0 num_threads_omp_pme 0 use_gpu False gpu_id Empty. gpu_tasks Empty. gmx_lib Empty. binary_path gmx
Step 21: MakeNdx input GRO,PDB,TPR file Output dataset 'output_gro_path' from step 20 input NDX file select at runtime output NDX name mymake_ndx.ndx Take tool settings: Manual Input Properties Input: selection \"Protein\"\|\"Other\" gmx_lib Empty. binary_path gmx
Step 22: GmxEnergy input EDR file Output dataset 'output_edr_path' from step 20 output XVG name mygmx_energy.xvg Take tool settings: Manual Input Properties Input: xvg none terms Potential binary_path gmx
Step 23: Grompp input GRO file Output dataset 'output_gro_path' from step 20 input ZIP file Output dataset 'output_top_zip_path' from step 18 input CPT file select at runtime input NDX file Output dataset 'output_ndx_path' from step 21 input MDP file select at runtime output TPR name mygrompp.tpr Take tool settings: Manual Input Properties Input: mdp {"nsteps": "5000", "tc-grps": "Protein_Other Water_and_ions", "Define": "-DPOSRES -DPOSRES_JZ4"} simulation_type nvt - substance N Volume V and Temperature T are conserved maxwarn 0 gmx_lib Empty. binary_path gmx
Step 24: Mdrun input TPR file Output dataset 'output_tpr_path' from step 23 input CPT file select at runtime output GRO name mymdrun.gro output EDR name mymdrun.edr output LOG name mymdrun.log output TRR name mymdrun.trr output XTC name mymdrun.xtc output CPT name mymdrun.cpt output XVG name mymdrun.xvg Take tool settings: Manual Input Properties Input: mpi_bin Empty. mpi_np 0 mpi_flags Empty. checkpoint_time 15 num_threads 0 num_threads_mpi 0 num_threads_omp 0 num_threads_omp_pme 0 use_gpu False gpu_id Empty. gpu_tasks Empty. gmx_lib Empty. binary_path gmx
Step 25: GmxEnergy input EDR file Output dataset 'output_edr_path' from step 24 output XVG name mygmx_energy.xvg Take tool settings: Manual Input Properties Input: xvg none terms Temperature binary_path gmx
Step 26: Grompp input GRO file Output dataset 'output_gro_path' from step 24 input ZIP file Output dataset 'output_top_zip_path' from step 18 input CPT file Output dataset 'output_cpt_path' from step 24 input NDX file Output dataset 'output_ndx_path' from step 21 input MDP file select at runtime output TPR name mygrompp.tpr Take tool settings: Manual Input Properties Input: mdp {"type": "npt", "nsteps": "5000", "tc-grps": "Protein_Other Water_and_ions", "Define": "-DPOSRES -DPOSRES_JZ4"} simulation_type npt - substance N pressure P and Temperature T are conserved maxwarn 0 gmx_lib Empty. binary_path gmx
Step 27: Mdrun input TPR file Output dataset 'output_tpr_path' from step 26 input CPT file select at runtime output GRO name mymdrun.gro output EDR name mymdrun.edr output LOG name mymdrun.log output TRR name mymdrun.trr output XTC name mymdrun.xtc output CPT name mymdrun.cpt output XVG name mymdrun.xvg Take tool settings: Manual Input Properties Input: mpi_bin Empty. mpi_np 0 mpi_flags Empty. checkpoint_time 15 num_threads 0 num_threads_mpi 0 num_threads_omp 0 num_threads_omp_pme 0 use_gpu False gpu_id Empty. gpu_tasks Empty. gmx_lib Empty. binary_path gmx
Step 28: GmxEnergy input EDR file Output dataset 'output_edr_path' from step 27 output XVG name mygmx_energy.xvg Take tool settings: Manual Input Properties Input: xvg none terms Pressure Density binary_path gmx
Step 29: Grompp input GRO file Output dataset 'output_gro_path' from step 27 input ZIP file Output dataset 'output_top_zip_path' from step 18 input CPT file Output dataset 'output_cpt_path' from step 27 input NDX file select at runtime input MDP file select at runtime output TPR name mygrompp.tpr Take tool settings: Manual Input Properties Input: mdp {"nsteps": "25000"} simulation_type free - No design constraints applied; Free MD maxwarn 0 gmx_lib Empty. binary_path gmx
Step 30: Mdrun input TPR file Output dataset 'output_tpr_path' from step 29 input CPT file select at runtime output GRO name mymdrun.gro output EDR name mymdrun.edr output LOG name mymdrun.log output TRR name mymdrun.trr output XTC name mymdrun.xtc output CPT name mymdrun.cpt output XVG name mymdrun.xvg Take tool settings: Manual Input Properties Input: mpi_bin Empty. mpi_np 0 mpi_flags Empty. checkpoint_time 15 num_threads 0 num_threads_mpi 0 num_threads_omp 0 num_threads_omp_pme 0 use_gpu False gpu_id Empty. gpu_tasks Empty. gmx_lib Empty. binary_path gmx
Step 31: GmxRgyr input TPR,GRO,G96,PDB,BRK,ENT file Output dataset 'output_tpr_path' from step 19 input XTC,TRR,CPT,GRO,G96,PDB,TNG file Output dataset 'output_trr_path' from step 30 input NDX file select at runtime output XVG name mygmx_rgyr.xvg Take tool settings: Manual Input Properties Input: xvg none selection Backbone - protein backbone atoms: N; C-alpha and C binary_path gmx
Step 32: GmxRms input TPR,GRO,G96,PDB,BRK,ENT file Output dataset 'output_tpr_path' from step 19 input XTC,TRR,CPT,GRO,G96,PDB,TNG file Output dataset 'output_trr_path' from step 30 input NDX file select at runtime output XVG name mygmx_rms.xvg Take tool settings: Manual Input Properties Input: xvg none selection Backbone - protein backbone atoms: N; C-alpha and C binary_path gmx
Step 33: GmxRms input TPR,GRO,G96,PDB,BRK,ENT file Output dataset 'output_tpr_path' from step 29 input XTC,TRR,CPT,GRO,G96,PDB,TNG file Output dataset 'output_trr_path' from step 30 input NDX file select at runtime output XVG name mygmx_rms_exp.xvg Take tool settings: Manual Input Properties Input: xvg none selection Backbone - protein backbone atoms: N; C-alpha and C binary_path gmx
Step 34: GmxTrjconvStr input XTC,TRR,CPT,GRO,G96,PDB,TNG file Output dataset 'output_trr_path' from step 30 input TPR,GRO,G96,PDB,BRK,ENT file Output dataset 'output_tpr_path' from step 29 input NDX file Output dataset 'output_ndx_path' from step 21 output PDB,XTC,TRR,CPT,GRO,G96,TNG name mygmx_trjconv_str.gro Take tool settings: Manual Input Properties Input: selection System - all atoms in the system pbc none - No PBC treatment center True ur compact - Puts all atoms at the closest distance from the center of the box fit none binary_path gmx output_format gro
Step 35: GmxImage input XTC,TRR,CPT,GRO,G96,PDB,TNG file Output dataset 'output_trr_path' from step 30 input TPR,GRO,G96,PDB,BRK,ENT file Output dataset 'output_tpr_path' from step 29 input NDX file Output dataset 'output_ndx_path' from step 21 output XTC,TRR,CPT,GRO,G96,PDB,TNG name mygmx_image.trr Take tool settings: Manual Input Properties Input: fit_selection Protein-H - protein atoms excluding hydrogens center_selection Protein-H - protein atoms excluding hydrogens cluster_selection System - all atoms in the system output_selection System - all atoms in the system pbc mol - Puts the center of mass of molecules in the box center True ur compact - Puts all atoms at the closest distance from the center of the box fit none binary_path gmx output_format trr

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GMX Protein Ligand Complex MD Setup

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