AMBER Protein MD Setup tutorials using BioExcel Building Blocks (biobb)
Based on the official GROMACS tutorial.
This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb) wrapping the Ambertools MD package.
Copyright & Licensing
This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728).
- (c) 2015-2022 Barcelona Supercomputing Center
- (c) 2015-2022 Institute for Research in Biomedicine
Licensed under the Apache License 2.0, see the file LICENSE for details.
Inputs
ID | Name | Description | Type |
---|---|---|---|
step1_leap_gen_top_config | n/a | n/a |
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step1_leap_gen_top_input_pdb_path | n/a | n/a |
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step1_leap_gen_top_output_pdb_path | n/a | n/a |
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step1_leap_gen_top_output_top_path | n/a | n/a |
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step1_leap_gen_top_output_crd_path | n/a | n/a |
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step2_leap_solvate_config | n/a | n/a |
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step2_leap_solvate_output_pdb_path | n/a | n/a |
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step2_leap_solvate_output_top_path | n/a | n/a |
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step2_leap_solvate_output_crd_path | n/a | n/a |
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step3_leap_add_ions_config | n/a | n/a |
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step3_leap_add_ions_output_pdb_path | n/a | n/a |
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step3_leap_add_ions_output_top_path | n/a | n/a |
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step3_leap_add_ions_output_crd_path | n/a | n/a |
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step4_cpptraj_randomize_ions_config | n/a | n/a |
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step4_cpptraj_randomize_ions_output_pdb_path | n/a | n/a |
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step4_cpptraj_randomize_ions_output_crd_path | n/a | n/a |
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step5_parmed_hmassrepartition_output_top_path | n/a | n/a |
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step6_sander_mdrun_eq1_config | n/a | n/a |
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step6_sander_mdrun_eq1_input_mdin_path | n/a | n/a |
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step6_sander_mdrun_eq1_output_traj_path | n/a | n/a |
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step6_sander_mdrun_eq1_output_rst_path | n/a | n/a |
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step6_sander_mdrun_eq1_output_log_path | n/a | n/a |
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step6_sander_mdrun_eq1_output_mdinfo_path | n/a | n/a |
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step7_process_minout_eq1_config | n/a | n/a |
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step7_process_minout_eq1_output_dat_path | n/a | n/a |
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step8_sander_mdrun_eq2_config | n/a | n/a |
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step8_sander_mdrun_eq2_input_mdin_path | n/a | n/a |
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step8_sander_mdrun_eq2_output_traj_path | n/a | n/a |
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step8_sander_mdrun_eq2_output_rst_path | n/a | n/a |
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step8_sander_mdrun_eq2_output_log_path | n/a | n/a |
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step8_sander_mdrun_eq2_output_mdinfo_path | n/a | n/a |
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step9_process_mdout_eq2_config | n/a | n/a |
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step9_process_mdout_eq2_output_dat_path | n/a | n/a |
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step10_sander_mdrun_eq3_config | n/a | n/a |
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step10_sander_mdrun_eq3_input_mdin_path | n/a | n/a |
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step10_sander_mdrun_eq3_output_traj_path | n/a | n/a |
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step10_sander_mdrun_eq3_output_rst_path | n/a | n/a |
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step10_sander_mdrun_eq3_output_log_path | n/a | n/a |
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step10_sander_mdrun_eq3_output_mdinfo_path | n/a | n/a |
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step11_process_minout_eq3_config | n/a | n/a |
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step11_process_minout_eq3_output_dat_path | n/a | n/a |
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step12_sander_mdrun_eq4_config | n/a | n/a |
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step12_sander_mdrun_eq4_input_mdin_path | n/a | n/a |
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step12_sander_mdrun_eq4_output_traj_path | n/a | n/a |
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step12_sander_mdrun_eq4_output_rst_path | n/a | n/a |
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step12_sander_mdrun_eq4_output_log_path | n/a | n/a |
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step12_sander_mdrun_eq4_output_mdinfo_path | n/a | n/a |
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step13_process_minout_eq4_config | n/a | n/a |
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step13_process_minout_eq4_output_dat_path | n/a | n/a |
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step14_sander_mdrun_eq5_config | n/a | n/a |
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step14_sander_mdrun_eq5_input_mdin_path | n/a | n/a |
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step14_sander_mdrun_eq5_output_traj_path | n/a | n/a |
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step14_sander_mdrun_eq5_output_rst_path | n/a | n/a |
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step14_sander_mdrun_eq5_output_log_path | n/a | n/a |
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step14_sander_mdrun_eq5_output_mdinfo_path | n/a | n/a |
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step15_process_minout_eq5_config | n/a | n/a |
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step15_process_minout_eq5_output_dat_path | n/a | n/a |
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step16_sander_mdrun_eq6_config | n/a | n/a |
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step16_sander_mdrun_eq6_input_mdin_path | n/a | n/a |
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step16_sander_mdrun_eq6_output_traj_path | n/a | n/a |
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step16_sander_mdrun_eq6_output_rst_path | n/a | n/a |
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step16_sander_mdrun_eq6_output_log_path | n/a | n/a |
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step16_sander_mdrun_eq6_output_mdinfo_path | n/a | n/a |
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step17_process_mdout_eq6_config | n/a | n/a |
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step17_process_mdout_eq6_output_dat_path | n/a | n/a |
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step18_sander_mdrun_eq7_config | n/a | n/a |
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step18_sander_mdrun_eq7_input_mdin_path | n/a | n/a |
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step18_sander_mdrun_eq7_output_traj_path | n/a | n/a |
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step18_sander_mdrun_eq7_output_rst_path | n/a | n/a |
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step18_sander_mdrun_eq7_output_log_path | n/a | n/a |
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step18_sander_mdrun_eq7_output_mdinfo_path | n/a | n/a |
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step19_process_mdout_eq7_config | n/a | n/a |
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step19_process_mdout_eq7_output_dat_path | n/a | n/a |
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step20_sander_mdrun_eq8_config | n/a | n/a |
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step20_sander_mdrun_eq8_input_mdin_path | n/a | n/a |
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step20_sander_mdrun_eq8_output_traj_path | n/a | n/a |
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step20_sander_mdrun_eq8_output_rst_path | n/a | n/a |
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step20_sander_mdrun_eq8_output_log_path | n/a | n/a |
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step20_sander_mdrun_eq8_output_mdinfo_path | n/a | n/a |
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step21_process_mdout_eq8_config | n/a | n/a |
|
step21_process_mdout_eq8_output_dat_path | n/a | n/a |
|
step22_sander_mdrun_eq9_config | n/a | n/a |
|
step22_sander_mdrun_eq9_input_mdin_path | n/a | n/a |
|
step22_sander_mdrun_eq9_output_traj_path | n/a | n/a |
|
step22_sander_mdrun_eq9_output_rst_path | n/a | n/a |
|
step22_sander_mdrun_eq9_output_log_path | n/a | n/a |
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step22_sander_mdrun_eq9_output_mdinfo_path | n/a | n/a |
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step23_process_mdout_eq9_config | n/a | n/a |
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step23_process_mdout_eq9_output_dat_path | n/a | n/a |
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step24_sander_mdrun_eq10_config | n/a | n/a |
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step24_sander_mdrun_eq10_input_mdin_path | n/a | n/a |
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step24_sander_mdrun_eq10_output_traj_path | n/a | n/a |
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step24_sander_mdrun_eq10_output_rst_path | n/a | n/a |
|
step24_sander_mdrun_eq10_output_log_path | n/a | n/a |
|
step24_sander_mdrun_eq10_output_mdinfo_path | n/a | n/a |
|
step25_process_mdout_eq10_config | n/a | n/a |
|
step25_process_mdout_eq10_output_dat_path | n/a | n/a |
|
step26_sander_mdrun_md_config | n/a | n/a |
|
step26_sander_mdrun_md_input_mdin_path | n/a | n/a |
|
step26_sander_mdrun_md_output_traj_path | n/a | n/a |
|
step26_sander_mdrun_md_output_rst_path | n/a | n/a |
|
step26_sander_mdrun_md_output_mdinfo_path | n/a | n/a |
|
step26_sander_mdrun_md_output_log_path | n/a | n/a |
|
Steps
ID | Name | Description |
---|---|---|
step1_leap_gen_top | LeapGenTop | Generates a MD topology from a molecule structure using tLeap tool from the AmberTools MD package |
step2_leap_solvate | LeapSolvate | Creates and solvates a system box for an AMBER MD system using tLeap tool from the AmberTools MD package |
step3_leap_add_ions | LeapAddIons | Adds counterions to a system box for an AMBER MD system using tLeap tool from the AmberTools MD package |
step4_cpptraj_randomize_ions | CpptrajRandomizeIons | Swap specified ions with randomly selected solvent molecules using cpptraj tool from the AmberTools MD package |
step5_parmed_hmassrepartition | ParmedHMassRepartition | Performs a Hydrogen Mass Repartition from an AMBER topology file using parmed tool from the AmberTools MD package |
step6_sander_mdrun_eq1 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step7_process_minout_eq1 | ProcessMinOut | Parses the AMBER (sander) minimization output file (log) and dumps statistics that can then be plotted. Using the process_minout.pl tool from the AmberTools MD package |
step8_sander_mdrun_eq2 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step9_process_mdout_eq2 | ProcessMDOut | Parses the AMBER (sander) md output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package |
step10_sander_mdrun_eq3 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step11_process_minout_eq3 | ProcessMinOut | Parses the AMBER (sander) minimization output file (log) and dumps statistics that can then be plotted. Using the process_minout.pl tool from the AmberTools MD package |
step12_sander_mdrun_eq4 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step13_process_minout_eq4 | ProcessMinOut | Parses the AMBER (sander) minimization output file (log) and dumps statistics that can then be plotted. Using the process_minout.pl tool from the AmberTools MD package |
step14_sander_mdrun_eq5 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step15_process_minout_eq5 | ProcessMinOut | Parses the AMBER (sander) minimization output file (log) and dumps statistics that can then be plotted. Using the process_minout.pl tool from the AmberTools MD package |
step16_sander_mdrun_eq6 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step17_process_mdout_eq6 | ProcessMDOut | Parses the AMBER (sander) md output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package |
step18_sander_mdrun_eq7 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step19_process_mdout_eq7 | ProcessMDOut | Parses the AMBER (sander) md output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package |
step20_sander_mdrun_eq8 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step21_process_mdout_eq8 | ProcessMDOut | Parses the AMBER (sander) md output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package |
step22_sander_mdrun_eq9 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step23_process_mdout_eq9 | ProcessMDOut | Parses the AMBER (sander) md output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package |
step24_sander_mdrun_eq10 | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
step25_process_mdout_eq10 | ProcessMDOut | Parses the AMBER (sander) md output file (log) and dumps statistics that can then be plotted. Using the process_mdout.pl tool from the AmberTools MD package |
step26_sander_mdrun_md | SanderMDRun | Runs energy minimization, molecular dynamics, and NMR refinements using sander tool from the AmberTools MD package |
Outputs
ID | Name | Description | Type |
---|---|---|---|
step1_leap_gen_top_out1 | output_pdb_path | Output 3D structure PDB file matching the topology file |
|
step1_leap_gen_top_out2 | output_top_path | Output topology file (AMBER ParmTop) |
|
step1_leap_gen_top_out3 | output_crd_path | Output coordinates file (AMBER crd) |
|
step2_leap_solvate_out1 | output_pdb_path | Output 3D structure PDB file matching the topology file |
|
step2_leap_solvate_out2 | output_top_path | Output topology file (AMBER ParmTop) |
|
step2_leap_solvate_out3 | output_crd_path | Output coordinates file (AMBER crd) |
|
step3_leap_add_ions_out1 | output_pdb_path | Output 3D structure PDB file matching the topology file |
|
step3_leap_add_ions_out2 | output_top_path | Output topology file (AMBER ParmTop) |
|
step3_leap_add_ions_out3 | output_crd_path | Output coordinates file (AMBER crd) |
|
step4_cpptraj_randomize_ions_out1 | output_pdb_path | Structure PDB file with randomized ions |
|
step4_cpptraj_randomize_ions_out2 | output_crd_path | Structure CRD file with coordinates including randomized ions |
|
step5_parmed_hmassrepartition_out1 | output_top_path | Output topology file (AMBER ParmTop) |
|
step6_sander_mdrun_eq1_out1 | output_traj_path | Output trajectory file |
|
step6_sander_mdrun_eq1_out2 | output_rst_path | Output restart file |
|
step6_sander_mdrun_eq1_out3 | output_log_path | Output log file |
|
step6_sander_mdrun_eq1_out4 | output_mdinfo_path | Output MD info |
|
step7_process_minout_eq1_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step8_sander_mdrun_eq2_out1 | output_traj_path | Output trajectory file |
|
step8_sander_mdrun_eq2_out2 | output_rst_path | Output restart file |
|
step8_sander_mdrun_eq2_out3 | output_log_path | Output log file |
|
step8_sander_mdrun_eq2_out4 | output_mdinfo_path | Output MD info |
|
step9_process_mdout_eq2_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step10_sander_mdrun_eq3_out1 | output_traj_path | Output trajectory file |
|
step10_sander_mdrun_eq3_out2 | output_rst_path | Output restart file |
|
step10_sander_mdrun_eq3_out3 | output_log_path | Output log file |
|
step10_sander_mdrun_eq3_out4 | output_mdinfo_path | Output MD info |
|
step11_process_minout_eq3_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step12_sander_mdrun_eq4_out1 | output_traj_path | Output trajectory file |
|
step12_sander_mdrun_eq4_out2 | output_rst_path | Output restart file |
|
step12_sander_mdrun_eq4_out3 | output_log_path | Output log file |
|
step12_sander_mdrun_eq4_out4 | output_mdinfo_path | Output MD info |
|
step13_process_minout_eq4_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step14_sander_mdrun_eq5_out1 | output_traj_path | Output trajectory file |
|
step14_sander_mdrun_eq5_out2 | output_rst_path | Output restart file |
|
step14_sander_mdrun_eq5_out3 | output_log_path | Output log file |
|
step14_sander_mdrun_eq5_out4 | output_mdinfo_path | Output MD info |
|
step15_process_minout_eq5_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step16_sander_mdrun_eq6_out1 | output_traj_path | Output trajectory file |
|
step16_sander_mdrun_eq6_out2 | output_rst_path | Output restart file |
|
step16_sander_mdrun_eq6_out3 | output_log_path | Output log file |
|
step16_sander_mdrun_eq6_out4 | output_mdinfo_path | Output MD info |
|
step17_process_mdout_eq6_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step18_sander_mdrun_eq7_out1 | output_traj_path | Output trajectory file |
|
step18_sander_mdrun_eq7_out2 | output_rst_path | Output restart file |
|
step18_sander_mdrun_eq7_out3 | output_log_path | Output log file |
|
step18_sander_mdrun_eq7_out4 | output_mdinfo_path | Output MD info |
|
step19_process_mdout_eq7_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step20_sander_mdrun_eq8_out1 | output_traj_path | Output trajectory file |
|
step20_sander_mdrun_eq8_out2 | output_rst_path | Output restart file |
|
step20_sander_mdrun_eq8_out3 | output_log_path | Output log file |
|
step20_sander_mdrun_eq8_out4 | output_mdinfo_path | Output MD info |
|
step21_process_mdout_eq8_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step22_sander_mdrun_eq9_out1 | output_traj_path | Output trajectory file |
|
step22_sander_mdrun_eq9_out2 | output_rst_path | Output restart file |
|
step22_sander_mdrun_eq9_out3 | output_log_path | Output log file |
|
step22_sander_mdrun_eq9_out4 | output_mdinfo_path | Output MD info |
|
step23_process_mdout_eq9_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step24_sander_mdrun_eq10_out1 | output_traj_path | Output trajectory file |
|
step24_sander_mdrun_eq10_out2 | output_rst_path | Output restart file |
|
step24_sander_mdrun_eq10_out3 | output_log_path | Output log file |
|
step24_sander_mdrun_eq10_out4 | output_mdinfo_path | Output MD info |
|
step25_process_mdout_eq10_out1 | output_dat_path | Dat output file containing data from the specified terms along the minimization process |
|
step26_sander_mdrun_md_out1 | output_traj_path | Output trajectory file |
|
step26_sander_mdrun_md_out2 | output_rst_path | Output restart file |
|
step26_sander_mdrun_md_out3 | output_mdinfo_path | Output MD info |
|
step26_sander_mdrun_md_out4 | output_log_path | Output log file |
|
Version History
Version 1 (earliest) Created 11th Jan 2022 at 08:14 by Genís Bayarri
Fetched sequence.pdb from URL
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Created: 11th Jan 2022 at 08:14
Last updated: 17th Mar 2022 at 10:44
Last used: 11th Aug 2022 at 23:23

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