Workflow Type: Galaxy
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Protein-ligand complex parameterization
Parameterizes an input protein (PDB) and ligand (SDF) file prior to molecular dynamics simulation with GROMACS.
This is a simple workflow intended for use as a subworkflow in more complex MD workflows. It is used as a subworkflow by the GROMACS MMGBSA and dcTMD workflows.
Inputs
ID | Name | Description | Type |
---|---|---|---|
Apoprotein PDB | Apoprotein PDB | PDB file for the protein (without ligand, cofactor, waters) |
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Force field | Force field | Force field for protein modelling. GAFF is used for the ligand. |
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Ligand SDF | Ligand SDF | SD-file for the input ligand |
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Water model | Water model | Model for water molecules (relevant for subsequent solvation) |
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pH | pH | pH for protonating the ligand. Set to -1.0 to skip. |
|
Steps
ID | Name | Description |
---|---|---|
5 | Compound conversion | toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0 |
6 | Descriptors | toolshed.g2.bx.psu.edu/repos/bgruening/ctb_rdkit_descriptors/ctb_rdkit_descriptors/2020.03.4+galaxy1 |
7 | GROMACS initial setup | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2021.3+galaxy0 |
8 | Search in textfiles | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1 |
9 | Cut | Cut1 |
10 | Parse parameter value | param_value_from_file |
11 | AnteChamber | toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_antechamber/ambertools_antechamber/21.10+galaxy0 |
12 | Generate MD topologies for small molecules | toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_acpype/ambertools_acpype/21.10+galaxy0 |
13 | Merge GROMACS topologies | toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/gmx_merge_topology_files/3.4.3+galaxy0 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
Position restraints file | Position restraints file | n/a |
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Complex topology | Complex topology | n/a |
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Complex GRO | Complex GRO | n/a |
|
Version History
v0.1.2 (latest) Created 21st Dec 2021 at 03:01 by WorkflowHub Bot
Updated to v0.1.2
Open
master
d8ca190
v0.1.1 (earliest) Created 7th Dec 2021 at 03:01 by WorkflowHub Bot
Added/updated 10 files
Frozen
master
f470798
Creators and Submitter
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Simon Bray
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Created: 7th Dec 2021 at 03:01
Last updated: 21st Dec 2021 at 03:01
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