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GMX Protein MD Setup

Annotation:

Step	Annotation
Step 1: Pdb output PDB name mypdb.pdb Take tool settings: Manual Input Properties Input: pdb_code 1AKI filter [ATOM, MODEL, ENDMDL] api_id pdbe - PDB in Europe REST API
Step 2: FixSideChain input PDB file Output dataset 'output_pdb_path' from step 1 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 3: Pdb2gmx input PDB file Output dataset 'output_pdb_path' from step 2 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 4: Editconf input GRO,PDB file Output dataset 'output_gro_path' from step 3 output PDB,GRO name myeditconf.gro Take tool settings: Manual Input Properties Input: distance_to_molecule 1.0 box_vector_lenghts Not available. box_type cubic - rectangular box with all sides equal center_molecule True gmx_lib Empty. binary_path gmx output_format gro
Step 5: Solvate input GRO,PDB file Output dataset 'output_gro_path' from step 4 input ZIP file Output dataset 'output_top_zip_path' from step 3 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 6: Grompp input GRO file Output dataset 'output_gro_path' from step 5 input ZIP file Output dataset 'output_top_zip_path' from step 5 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 {} simulation_type minimization - Energy minimization using steepest descent algorithm is used maxwarn 1 gmx_lib Empty. binary_path gmx
Step 7: Genion input TPR file Output dataset 'output_tpr_path' from step 6 input ZIP file Output dataset 'output_top_zip_path' from step 5 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 8: Grompp input GRO file Output dataset 'output_gro_path' from step 7 input ZIP file Output dataset 'output_top_zip_path' from step 7 input CPT file select at runtime input NDX file select at runtime input MDP file select at runtime output TPR name mygrompp_min.tpr Take tool settings: Manual Input Properties Input: mdp {"emtol":"500", "nsteps":"5000"} simulation_type minimization - Energy minimization using steepest descent algorithm is used maxwarn 1 gmx_lib Empty. binary_path gmx
Step 9: Mdrun input TPR file Output dataset 'output_tpr_path' from step 8 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 10: Grompp input GRO file Output dataset 'output_gro_path' from step 9 input ZIP file Output dataset 'output_top_zip_path' from step 7 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,"dt": 0.002,"Define": "-DPOSRES"} simulation_type nvt - substance N Volume V and Temperature T are conserved maxwarn 0 gmx_lib Empty. binary_path gmx
Step 11: GmxEnergy input EDR file Output dataset 'output_edr_path' from step 9 output XVG name mygmx_energy.xvg Take tool settings: Manual Input Properties Input: xvg none terms Potential binary_path gmx
Step 12: Mdrun input TPR file Output dataset 'output_tpr_path' from step 10 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 13: Grompp input GRO file Output dataset 'output_gro_path' from step 12 input ZIP file Output dataset 'output_top_zip_path' from step 7 input CPT file Output dataset 'output_cpt_path' from step 12 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"} simulation_type npt - substance N pressure P and Temperature T are conserved maxwarn 0 gmx_lib Empty. binary_path gmx
Step 14: GmxEnergy input EDR file Output dataset 'output_edr_path' from step 12 output XVG name mygmx_energy.xvg Take tool settings: Manual Input Properties Input: xvg none terms Temperature binary_path gmx
Step 15: Mdrun input TPR file Output dataset 'output_tpr_path' from step 13 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 16: Grompp input GRO file Output dataset 'output_gro_path' from step 15 input ZIP file Output dataset 'output_top_zip_path' from step 7 input CPT file Output dataset 'output_cpt_path' from step 15 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":"50000"} simulation_type free - No design constraints applied; Free MD maxwarn 0 gmx_lib Empty. binary_path gmx
Step 17: GmxEnergy input EDR file Output dataset 'output_edr_path' from step 15 output XVG name mygmx_energy.xvg Take tool settings: Manual Input Properties Input: xvg none terms Pressure Density binary_path gmx
Step 18: Mdrun input TPR file Output dataset 'output_tpr_path' from step 16 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 19: GmxRms input TPR,GRO,G96,PDB,BRK,ENT file Output dataset 'output_tpr_path' from step 8 input XTC,TRR,CPT,GRO,G96,PDB,TNG file Output dataset 'output_trr_path' from step 18 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 20: GmxRms input TPR,GRO,G96,PDB,BRK,ENT file Output dataset 'output_tpr_path' from step 16 input XTC,TRR,CPT,GRO,G96,PDB,TNG file Output dataset 'output_trr_path' from step 18 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 21: GmxRgyr input TPR,GRO,G96,PDB,BRK,ENT file Output dataset 'output_tpr_path' from step 8 input XTC,TRR,CPT,GRO,G96,PDB,TNG file Output dataset 'output_trr_path' from step 18 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 22: GmxImage input XTC,TRR,CPT,GRO,G96,PDB,TNG file Output dataset 'output_trr_path' from step 18 input TPR,GRO,G96,PDB,BRK,ENT file Output dataset 'output_tpr_path' from step 16 input NDX file select at runtime output XTC,TRR,CPT,GRO,G96,PDB,TNG name mygmx_image.trr Take tool settings: Manual Input Properties Input: fit_selection System - all atoms in the system center_selection Protein - all protein atoms cluster_selection System - all atoms in the system output_selection Protein - all protein atoms 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
Step 23: GmxTrjconvStr input XTC,TRR,CPT,GRO,G96,PDB,TNG file Output dataset 'output_gro_path' from step 18 input TPR,GRO,G96,PDB,BRK,ENT file Output dataset 'output_tpr_path' from step 16 input NDX file select at runtime output PDB,XTC,TRR,CPT,GRO,G96,TNG name mygmx_trjconv_str.gro Take tool settings: Manual Input Properties Input: selection Protein - all protein atoms 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

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gbayarri

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GMX Protein MD Setup

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