Re: [AMBER] PBSA error

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Thu, 20 Nov 2014 14:49:07 -0800

Interesting … please email me your files (inpcrd type with prmtop
file) off the list so I can take a look …

All the best,
Ray

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, Chemical Physics,
Chemical and Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Thu, Nov 20, 2014 at 12:52 PM, Kshatresh Dutta Dubey
<kshatresh.gmail.com> wrote:
> Hi Jason and David,
>
> I re-ran the pbsa using old styled inpcrd, but unfortunately I am getting
> same error.
>
> Regards
> Kshatresh
>
> On Thu, Nov 20, 2014 at 10:45 PM, Kshatresh Dutta Dubey <kshatresh.gmail.com
>> wrote:
>
>> Thanks David and Jason for your suggestions.
>>
>> Regards
>> Kshatresh
>>
>> On Thu, Nov 20, 2014 at 10:42 PM, David A Case <case.biomaps.rutgers.edu>
>> wrote:
>>
>>> > On Thu, Nov 20, 2014, Kshatresh Dutta Dubey wrote:
>>> > >
>>> > > I am using amber 14 for pbsa program. When I am trying to run the
>>> pbsa with
>>> > > :
>>> > > pbsa -O -i pbsa.in -o pbsa.out -p ../dimer-sb-wat.prmtop -c
>>> > > dimer-SB-run1.rst &
>>> > >
>>> > > It is showing error:
>>> > > Program received signal SIGSEGV: Segmentation fault - invalid memory
>>> > > reference.
>>> >
>>> > > segmentation fault. I am using netcdf format of rst file...
>>> >
>>> > Try converting the rst file to the older (formatted) format: in cpptraj
>>> >
>>> > trajin dimer-SB-run1.rst
>>> > trajin dimer-SB-run1.rst7 restart
>>>   ^^^^^^^  <=   trajout here, not trajin.....
>>>
>>> ...dac
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>>
>>
>>
>
>
> --
> With best regards
> ************************************************************************************************
> Kshatresh Dutta Dubey
> Post Doctoral Researcher,
> Lise Meitner Center for Computational Quantum Chemistry
> Hebrew University of Jerusalem Israel
> Jerusalem, Israel
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

Received on Thu Nov 20 2014 - 15:00:02 PST