Error in gmx_MMPBSA for protein-protein complex

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Nupur Nagar

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Mar 19, 2022, 2:56:09 AM3/19/22

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I am getting an error while running gmx_MMPBSA command for a protein-protein complex. I have attached the screenshot of error and parameter file for the reference. Please help me troubleshoot this error. I ran the MD simulation using Charmm36 ff in Gromacs 2020.5.

mmpbsa.in

marioe911116

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Mar 19, 2022, 5:07:09 PM3/19/22

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Hi there! when working with systems prepared with CHARMM force field, it is mandatory to define the topology with the flag '-cp' in the command line... in your case it will be somehting like this:

gmx_MMPBSA -O -i mmpbsa.in -cs md_500.tpr -ci index.ndx -cg 18 19 -ct md_500_nojump.xtc -cp topol.top

where topol.top (change this name accordingly) is the topology of your system...

cheers!

Mario E.

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