gromacs-mmgbsa/main

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GROMACS MMGBSA free energy calculation

Perform an ensemble of MD simulations of a user-specified size using GROMACS, and calculate MMGBSA free energies using AmberTools. An ensemble average is calculated and returned to the user as the final input.

The input protein (PDB) and ligand (SDF) files provided are parameterized by the 'Protein-ligand complex parameterization' subworkflow.

SEEK ID: https://workflowhub.eu/workflows/248?version=1

Inputs

ID Name Description Type
Apoprotein PDB Apoprotein PDB PDB input
  • File
Force field Force field Force field
  • string
Ligand SDF Ligand SDF SDF input
  • File
NPT equilibration steps NPT equilibration steps Number of steps for NPT equilibration
  • int
NVT equilibration steps NVT equilibration steps Number of steps for NVT equilibration
  • int
Number of simulations Number of simulations Size of the MMGBSA ensemble
  • int
Production steps Production steps Number of steps for production simulation
  • int
Salt concentration Salt concentration NaCl concentration
  • float?
Water model Water model Water model
  • string
pH pH pH for protonation (-1.0 to skip)
  • float?

Steps

ID Name Description
10 Compose text parameter value toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
11 Create GRO and TOP complex files d354bc62a13564f8
12 Create text file toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0
13 GROMACS structure configuration toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2021.3+galaxy0
14 Split file toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0
15 Parse parameter value param_value_from_file
16 GROMACS solvation and adding ions toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2021.3+galaxy1
17 GROMACS energy minimization toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2021.3+galaxy1
18 Convert Parameters toolshed.g2.bx.psu.edu/repos/chemteam/parmconv/parmconv/21.10+galaxy0
19 GROMACS simulation toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2021.3+galaxy2
20 GROMACS simulation toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2021.3+galaxy2
21 GROMACS simulation toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2021.3+galaxy2
22 MDTraj file converter toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.6+galaxy0
23 MMPBSA/MMGBSA toolshed.g2.bx.psu.edu/repos/chemteam/mmpbsa_mmgbsa/mmpbsa_mmgbsa/21.10+galaxy0
24 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
25 Collapse Collection toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2
26 Cut Cut1
27 Summary Statistics Summary_Statistics1

Outputs

ID Name Description Type
Complex topology Complex topology n/a
  • File
Complex GRO Complex GRO n/a
  • File
GROMACS setup (ITP) on input dataset(s) GROMACS setup (ITP) on input dataset(s) n/a
  • File
GRO files GRO files n/a
  • File
XTC files XTC files n/a
  • File
MMGBSA statistics MMGBSA statistics n/a
  • File
MMGBSA free energy MMGBSA free energy n/a
  • File

Version History

v0.1.5 (latest) Created 28th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.1.5


Frozen v0.1.5 1115a7a

v0.1.4 Created 24th Nov 2023 at 03:02 by WorkflowHub Bot

Updated to v0.1.4


Frozen v0.1.4 6c9fb6b

v0.1.2 Created 21st Dec 2021 at 03:01 by WorkflowHub Bot

Updated to v0.1.2


Open master 2d38c00

v0.1.1 (earliest) Created 7th Dec 2021 at 03:01 by WorkflowHub Bot

Added/updated 8 files


Frozen master fbebd11
help Creators and Submitter
Creator
  • Simon Bray
Additional credit

Simon Bray

Submitter
Tools
Gromacs
AmberTools
License
MIT License (MIT)
Activity

Views: 11541   Downloads: 7137   Runs: 27

Created: 7th Dec 2021 at 03:01

Last updated: 24th Nov 2023 at 03:02

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