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
OpenMM MM/GBSA calculations
- Peter Eastman
- Posts: 2583
- Joined: Thu Aug 09, 2007 1:25 pm
Re: OpenMM MM/GBSA calculations
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
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
- Posts: 3
- Joined: Fri Oct 16, 2020 11:20 am
Re: OpenMM MM/GBSA calculations
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
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
- Posts: 2583
- Joined: Thu Aug 09, 2007 1:25 pm
Re: OpenMM MM/GBSA calculations
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
- Posts: 63
- Joined: Tue Mar 06, 2018 8:56 pm
Re: OpenMM MM/GBSA calculations
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/
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
- Posts: 63
- Joined: Tue Mar 06, 2018 8:56 pm
Re: OpenMM MM/GBSA calculations
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
https://github.com/ljmartin/mmpbsa_from_openmm
- Osvaldo Yáñez
- Posts: 3
- Joined: Fri Oct 16, 2020 11:20 am
Re: OpenMM MM/GBSA calculations
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
CaFE looks like a good tool and thanks for presenting it to me.
Greetings