Workflow Type: Galaxy

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)
  • File
Force field Force field Force field for protein modelling. GAFF is used for the ligand.
  • string
Ligand SDF Ligand SDF SD-file for the input ligand
  • File
Water model Water model Model for water molecules (relevant for subsequent solvation)
  • string
pH pH pH for protonating the ligand. Set to -1.0 to skip.
  • float?

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
  • File
Complex topology Complex topology n/a
  • File
Complex GRO Complex GRO n/a
  • File

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
help Creators and Submitter
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Simon Bray

Submitter
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Views: 3467   Downloads: 323   Runs: 0

Created: 7th Dec 2021 at 03:01

Last updated: 21st Dec 2021 at 03:01

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