MM-GBSA and MM-PBSA for Gromacs 2020

User discussions
1

GROMACS version: 2020.1
GROMACS modification: No

Hello all,

I am performing a protein-ligand simulation, and I would like to use MM-GBSA or MM-PBSA to perform free energy calculations. I know that there is the g_mmpbsa (https://rashmikumari.github.io/g_mmpbsa/) package available on GitHub, but it’s apparently incompatible with files in Gromacs-2020 (when I tried to use it, it gave me a clear error stating that I was trying to input files from version 113 [I think?] into a program whose version is 109).

Does anyone know of any alternative way of running MM-GBSA or MM-PBSA calculations on MD output files from Gromacs version 2020.1?

If there is no such way to do that, does anyone know of any other way to calculate free energy after the simulation is finished? (I have already finished my simulations, and I am hoping to not have to run them again.)

Thank you so much for your help,
Surya

2

Using the GMXPBSA scripts (https://github.com/aspitaleri/gmxpbsa) can be a good alternative.

Sandor

3

i install version of 2.1.2 GMXMMPBSA in Ubuntu 2020.4 and create INPUT.dat but get this error.
The Folder = that you indicated in the INPUT.dat file does not exist.
Exiting…
INPUT.dat (982 Bytes)

4

Can you please tell how did you rectify this error as I’m facing this same issue. Kindly help.

5

After playing around with the scripts, I realized that it was an issue concerning the format/syntax of the INPUT.dat. You can refer to GitHub - aspitaleri/gmxpbsa_demo: Demo file to test the gmxpbsa installation for the examples of how INPUT.dat should be written.