MD protein-ligand workflow (from PDB structure)
2.0

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Workflow Type: Galaxy

High Throughput Molecular Dynamics and Analysis

Associated Tutorial

This workflows is part of the tutorial MD protein-ligand workflow (from PDB structure), available in the GTN

Thanks to...

Tutorial Author(s): Simon Bray, Tharindu Senapathi, Christopher Barnett, Björn Grüning

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SEEK ID: https://dev.workflowhub.eu/workflows/1134?version=1

Inputs

ID Name Description Type
Ligand name (e.g. AG5E) Ligand name (e.g. AG5E) n/a
  • string
PDB code (e.g. 6hhr) PDB code (e.g. 6hhr) n/a
  • string

Steps

ID Name Description
2 Get PDB file toolshed.g2.bx.psu.edu/repos/bgruening/get_pdb/get_pdb/0.1.0
3 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
4 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
5 GROMACS initial setup toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2019.1.4
6 Compound conversion toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert/2.4.2.2.0
7 Generate MD topologies for small molecules toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_acpype/ambertools_acpype/19.11
8 Merge GROMACS topologies toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/gmx_merge_topology_files/3.2.0
9 GROMACS structure configuration toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2019.1.4
10 GROMACS solvation and adding ions toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2019.1.4
11 GROMACS energy minimization toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2019.1.4
12 GROMACS simulation toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4.1
13 GROMACS simulation toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4.1
14 GROMACS simulation toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2019.1.4.1

Version History

2.0 (earliest) Created 25th Jun 2024 at 11:02 by Helena Rasche

Added/updated 4 files


Open master 834ab8f
help Creators and Submitter
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Submitter
Discussion Channel
GTN Matrix
Tools
The Protein Data Bank (PDB)
Gromacs
Open Babel
AmberTools
License
Creative Commons Attribution 4.0 International (CC-BY-4.0)
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Views: 1032   Downloads: 276   Runs: 0

Created: 25th Jun 2024 at 11:01

Last updated: 25th Jun 2024 at 11:02

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