[gmx-users] Free energy calculation by MM_PBSA

[Indu Kumari]

Thank you.


With regards,
Indu

On Tue, Dec 9, 2014 at 12:59 PM, Bikash Ranjan Sahoo <
bikash.bioinformatics at gmail.com> wrote:

> Hi,
> 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.
>
> ----------------------------------------------------------
> *BIKASH RANJAN SAHOO *
>
> *​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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