OpenMM MM/GBSA calculations

[Osvaldo Yáñez]

Hello OPENMM team, along with greeting you, I wanted to ask you if there is any protocol for MMGBSA calculations that can be used?

Greetings

[Peter Eastman]

If you're starting from Amber or CHARMM files, we support a variety of GB models:

http://docs.openmm.org/latest/userguide ... it-solvent

If you're starting from a PDB file, we provide an implementation of OBC for most of the older Amber force fields, although not Amber14:

http://docs.openmm.org/latest/userguide ... rce-fields

[Osvaldo Yáñez]

Thank you for your quick response, Peter.

I have another question, if openMM has any script in python (e.g., MMPBSA.py with AmberTools ) to run the protocol in MMGBSA.

Regards

[Peter Eastman]

Which protocol are you referring to? GBSA defines how you calculate forces and energies. What you do with it depends on what you want to calculate.

[lewis martin]

I think that's referring to estimating free energies of ligand binding using MMPBSA.

Since this is a post-processing technique, Osvaldo you can use any of the analysis toolkits out there on the trajectories you generate with OpenMM:

-For example MMPBSA.py from the AMBER toolkit like you mentioned.
-Alternatively if you're using a PSF file with CHARMM parameters you can use CaFE plugin for VMD: https://github.com/huiliucode/cafe_plugin
-GROMACS-style files like TPR and XTC can be analysed with g_mmpbsa: https://rashmikumari.github.io/g_mmpbsa/

[lewis martin]

Actually I wanted to do this for a while so here's a repo demonstrating how to use OpenForceField, OpenMM, and CaFE to run an MMPBSA estimate of the binding affinity of catechol to T4 Lysozyme

https://github.com/ljmartin/mmpbsa_from_openmm

[Osvaldo Yáñez]

Thank you very much Peter Eastman and Lewis Martin, it was just what I needed to do the MMGBSA calculations.

CaFE looks like a good tool and thanks for presenting it to me.

Greetings