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

gtn star logo followed by the word workflows

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
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
The Protein Data Bank (PDB)
Gromacs
Open Babel
AmberTools
License
Creative Commons Attribution 4.0 International
Activity

Views: 311   Downloads: 82

Created: 25th Jun 2024 at 11:01

Last updated: 25th Jun 2024 at 11:02

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