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.

Changelog

[0.1.5] 2023-11-27

Automatic update

• toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2021.3+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup/2022+galaxy0
• toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2021.3+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2022+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.0 was updated to toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1
• toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2021.3+galaxy1 was updated to toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2022+galaxy0
• toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2021.3+galaxy1 was updated to toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2022+galaxy0
• toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2021.3+galaxy2 was updated to toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0
• toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.6+galaxy0 was updated to toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.7+galaxy0
• toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/4.2 was updated to toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0

[0.1.4] 2023-11-20

• Fix author in dockstore
• Fix changeset_revision of gmx_solvate

[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 GROMACS MMGBSA 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/iuc/compose_text_param/compose_text_param/0.1.1
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines/1.1.0
• toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf/2022+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1
• param_value_from_file
• toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate/2022+galaxy0
• toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2022+galaxy0
• toolshed.g2.bx.psu.edu/repos/chemteam/parmconv/parmconv/21.10+galaxy0
• toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0
• toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter/1.9.6+galaxy0
• toolshed.g2.bx.psu.edu/repos/chemteam/mmpbsa_mmgbsa/mmpbsa_mmgbsa/21.10+galaxy0
• toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
• toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset/5.1.0
• Cut1
• Summary_Statistics1