AMBER Constant pH MD setup tutorial using BioExcel Building Blocks (biobb)
Version 1

Workflow Type: Jupyter

This tutorial aims to illustrate the process of setting up a simulation system to run constant pH Molecular Dynamics simulations with AMBER, step by step, using the BioExcel Building Blocks library (biobb) wrapping the AmberTools utility from the AMBER package. The particular example used is the Bovine Pancreatic Trypsin Inhibitor (BPTI) protein (PDB code 6PTI).

Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliar libraries used are: nbcondakernels, nglview, ipywidgets, plotly, and simpletraj. Environment can be setup using the included environment.yml file.



Parameters needed to configure the workflow:

  • pdbCode: PDB code of the experimental complex structure (if exists).


Output files generated (named according to the input parameters given above):

  • output_pH_dat_path: Predicted pKa values extracted from the constant pH MD simulation.
  • output_pH_pop_path: Populations of every state for every titratable residue, fraction of snapshots that the system spent in each state for each residue.
help Creators and Submitter
Bayarri, G., & Hospital, A. (2021). AMBER Constant pH MD setup tutorial using BioExcel Building Blocks (biobb) (jupyter notebook). WorkflowHub.

Views: 261   Downloads: 7

Created: 30th Jun 2021 at 13:23

Last updated: 8th Jul 2021 at 10:10

Last used: 15th Oct 2021 at 22:29

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Version 1 Created 30th Jun 2021 at 13:23 by Genís Bayarri

Initial commit. Taken from Git commit 5ae6892

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