[gmx-users] Free energy calculation by MM_PBSA

[Indu Kumari]

Hello everyone,

I tried to do it for single (snapshot) .trr file, but the error is same,
SEGMENTATION FAULT. I am not able to figure out problem.

With regards,
Indu

On Tue, Dec 9, 2014 at 1:56 PM, Indu Kumari <kumari.indu31 at gmail.com> wrote:
>
> 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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