Workflow Type: Galaxy

MMGBSA simulation and calculation

Inputs

ID Name Description Type
Apoprotein PDB #main/Apoprotein PDB PDB input
  • File
Force field #main/Force field Force field
  • string
Ligand SDF #main/Ligand SDF SDF input
  • File
NPT equilibration steps #main/NPT equilibration steps Number of steps for NPT equilibration
  • int
NVT equilibration steps #main/NVT equilibration steps Number of steps for NVT equilibration
  • int
Number of simulations #main/Number of simulations Size of the MMGBSA ensemble
  • int
Production steps #main/Production steps Number of steps for production simulation
  • int
Salt concentration #main/Salt concentration NaCl concentration
  • float
Water model #main/Water model Water model
  • string
pH #main/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 n/a
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/2022+galaxy0
14 Split file toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.1
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/2022+galaxy0
17 GROMACS energy minimization toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em/2022+galaxy0
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/2022+galaxy0
20 GROMACS simulation toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0
21 GROMACS simulation toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim/2022+galaxy0
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/5.1.0
26 Cut Cut1
27 Summary Statistics Summary_Statistics1

Outputs

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

Views: 3299

Created: 7th Dec 2021 at 03:01

Last updated: 24th Nov 2023 at 03:02

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