How to run MMPBSA by gromos forcefield toplogy and gromacs 2023.2?

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Milad Bagheri

https://rashmikumari.github.io/g_mmpbsa/

Jobin Thomas

Milad Bagheri this algorithm will not work for Gromacs version 2019 and above....

use the gmx_MMPBSA module for the same

(https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/)

Regards

Benyamin Moraditabar

Jobin Thomas Unfortunately the gmx_MMPBSA module does not work with gromos forcefields

Arpit Jain

To fix the "Not all bond parameters found" error in GROMACS with GROMOS force field:

Check Topology: Ensure the GROMOS 43a1.ff topology includes all parameters.

Preprocess: Use gmx pdb2gmx to regenerate the topology with the correct force field.

Files: Ensure correct use of .xtc and .top files.

gmx_mmpbsa Compatibility: Verify that the version supports GROMOS force fields.

all of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.