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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

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

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

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.

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/

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

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