protein-ligand-complex-parameterization/main
v0.1.1 (earliest)

v0.1.2 (latest)

v0.1.1 (earliest)

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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.

SEEK ID: https://workflowhub.eu/workflows/247?version=1

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