Workflow Type: Galaxy
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MMGBSA simulation and calculation
Inputs
ID | Name | Description | Type |
---|---|---|---|
Apoprotein PDB | #main/Apoprotein PDB | PDB input |
|
Force field | #main/Force field | Force field |
|
Ligand SDF | #main/Ligand SDF | SDF input |
|
NPT equilibration steps | #main/NPT equilibration steps | Number of steps for NPT equilibration |
|
NVT equilibration steps | #main/NVT equilibration steps | Number of steps for NVT equilibration |
|
Number of simulations | #main/Number of simulations | Size of the MMGBSA ensemble |
|
Production steps | #main/Production steps | Number of steps for production simulation |
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Salt concentration | #main/Salt concentration | NaCl concentration |
|
Water model | #main/Water model | Water model |
|
pH | #main/pH | pH for protonation (-1.0 to skip) |
|
Steps
ID | Name | Description |
---|---|---|
10 | Compose text parameter value | toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1 |
11 | Create GRO and TOP complex files | n/a |
12 | Create text file | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0 |
13 | GROMACS structure configuration | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2022+galaxy0 |
14 | Split file | toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1 |
15 | Parse parameter value | param_value_from_file |
16 | GROMACS solvation and adding ions | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2022+galaxy0 |
17 | GROMACS energy minimization | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2022+galaxy0 |
18 | Convert Parameters | toolshed.g2.bx.psu.edu/repos/chemteam/parmconv/parmconv/21.10+galaxy0 |
19 | GROMACS simulation | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0 |
20 | GROMACS simulation | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0 |
21 | GROMACS simulation | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0 |
22 | MDTraj file converter | toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.6+galaxy0 |
23 | MMPBSA/MMGBSA | toolshed.g2.bx.psu.edu/repos/chemteam/mmpbsa_mmgbsa/mmpbsa_mmgbsa/21.10+galaxy0 |
24 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
25 | Collapse Collection | toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0 |
26 | Cut | Cut1 |
27 | Summary Statistics | Summary_Statistics1 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
Complex GRO | #main/Complex GRO | n/a |
|
Complex topology | #main/Complex topology | n/a |
|
GRO files | #main/GRO files | n/a |
|
GROMACS setup (ITP) on input dataset(s) | #main/GROMACS setup (ITP) on input dataset(s) | n/a |
|
MMGBSA free energy | #main/MMGBSA free energy | n/a |
|
MMGBSA statistics | #main/MMGBSA statistics | n/a |
|
XTC files | #main/XTC files | n/a |
|
Version History
v0.1.5 (latest) Created 28th Nov 2023 at 03:02 by WorkflowHub Bot
Updated to v0.1.5
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v0.1.5
1115a7a
v0.1.1 (earliest) Created 7th Dec 2021 at 03:01 by WorkflowHub Bot
Added/updated 8 files
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master
fbebd11
Creators and Submitter
Creator
Additional credit
Simon Bray
Submitter
Tools
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Activity
Views: 6659 Downloads: 644 Runs: 0
Created: 7th Dec 2021 at 03:01
Last updated: 24th Nov 2023 at 03:02
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