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Tests GROMACS MMGBSA free energy calculation
Perform an ensemble of MD simulations of a user-specified size using GROMACS, and calculate MMGBSA free energies using AmberTools. An ensemble average is calculated and returned to the user as the final input.
The input protein (PDB) and ligand (SDF) files provided are parameterized by the 'Protein-ligand complex parameterization' subworkflow.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Apoprotein PDB | Apoprotein PDB | PDB input |
|
| Force field | Force field | Force field |
|
| Ligand SDF | Ligand SDF | SDF input |
|
| NPT equilibration steps | NPT equilibration steps | Number of steps for NPT equilibration |
|
| NVT equilibration steps | NVT equilibration steps | Number of steps for NVT equilibration |
|
| Number of simulations | Number of simulations | Size of the MMGBSA ensemble |
|
| Production steps | Production steps | Number of steps for production simulation |
|
| Salt concentration | Salt concentration | NaCl concentration |
|
| Water model | Water model | Water model |
|
| pH | 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 | d354bc62a13564f8 |
| 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/2021.3+galaxy0 |
| 14 | Split file | toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 |
| 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/2021.3+galaxy1 |
| 17 | GROMACS energy minimization | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2021.3+galaxy1 |
| 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/2021.3+galaxy2 |
| 20 | GROMACS simulation | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2021.3+galaxy2 |
| 21 | GROMACS simulation | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2021.3+galaxy2 |
| 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/4.2 |
| 26 | Cut | Cut1 |
| 27 | Summary Statistics | Summary_Statistics1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| Complex topology | Complex topology | n/a |
|
| Complex GRO | Complex GRO | n/a |
|
| GROMACS setup (ITP) on input dataset(s) | GROMACS setup (ITP) on input dataset(s) | n/a |
|
| GRO files | GRO files | n/a |
|
| XTC files | XTC files | n/a |
|
| MMGBSA statistics | MMGBSA statistics | n/a |
|
| MMGBSA free energy | MMGBSA free energy | 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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v0.1.51115a7a
v0.1.1 (earliest) Created 7th Dec 2021 at 03:01 by WorkflowHub Bot
Added/updated 8 files
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masterfbebd11
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Views: 6909 Downloads: 692 Runs: 0
Created: 7th Dec 2021 at 03:01
Last updated: 24th Nov 2023 at 03:02
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