[gmx-users] Free energy calculation by MM_PBSA

Bikash Ranjan Sahoo bikash.bioinformatics at gmail.com
Tue Dec 9 08:30:24 CET 2014

This usually occurred when you run apbs for a large number of conformations
serially. Sometimes, a big protein (800-1000 residues) also arrested the
program as apbs consumes a very high memory on cluster (in my case for 500
snapshots ~400 aa long protein it consumes ~300-400GB). Try using a small
number of snapshots if you are running in parallel. And if you are running
one pro, lig and complex in your local computer, kindly check the CPU usage
and do the needful. Core dumped usually  fired with memory inadequacy.


*​Osaka Univ. Japan​*

On Tue, Dec 9, 2014 at 4:16 PM, Indu Kumari <kumari.indu31 at gmail.com> wrote:

> Hello everyone,
> I am trying to calculate free energy of protein ligand complex by using
> MM_PBSA method. While calculating polar solvation energy of the complex, I
> am getting this error.
> * Segmentation fault (core dumped).*
> *Please help!*
> With regards,
> Indu
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