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.

Changelog

[0.1.4] 2023-11-20

• Fix author in dockstore

[0.1.3] 2022-05-25

Changed

• Changed creator ORCID to absolute URI

[0.1.2] 2021-12-13

Added

• Added GitHub Actions workflow. No functional changes.

[0.1.1] 2021-12-06

Fixed

• .workflowhub.yml: use repo-name/dockstore-workflow-name scheme for workflows.
• Moved test data inside repo.

[0.1]

• Initial version of protein-ligand parameterization workflow.

The following tools are required to run this workflow.

This will eventually be a pretty page with links to each tool in the (new) toolshed, etc.

• toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/3.1.1+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/ctb_rdkit_descriptors/ctb_rdkit_descriptors/2020.03.4+galaxy1
• toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2021.3+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
• Cut1
• param_value_from_file
• toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_antechamber/ambertools_antechamber/21.10+galaxy0
• toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_acpype/ambertools_acpype/21.10+galaxy0
• toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/gmx_merge_topology_files/3.4.3+galaxy0