Apologies to burden the list with this problem.
I’ve run MMPBSA.py.MPI on a different simulation. I encountered the same problem. Please see attached mdout and log files.
I wonder if I should recompile and run MMPBSA again.
Your suggestions will be most welcome.
Regards
George
On Feb 25, 2014, at 9:56 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Apologies for my oversight. The file is now attached.
>
> Thank you for your help
>
> Regards
>
> George
>
> <MMPBSA-abort.zip>
> On Feb 25, 2014, at 8:58 PM, Jason Swails <jason.swails.gmail.com> wrote:
>
>>
>>
>>> On Feb 25, 2014, at 5:16 PM, George Tzotzos <gtzotzos.me.com> wrote:
>>>
>>> Jason, Bill,
>>>
>>> Thanks a lot. I have made several repetitions. It always hangs.
>>>
>>> In the last couple, it aborted on rank 10. I’m attaching the _MMPBSA_complex_gb.mdout.10 and 11.
>>> I’m also attaching the input script. In the last run, I set mol surf=1
>>> Finally, I’m also attaching the prmtop and inpcrd files.
>>>
>>> Once again thanks for looking into the problem.
>>
>> I think cpptraj is having a problem with the surface area calculation (the error occurs on whatever thread starts cpptraj first).
>>
>> Also, I don't see any attachments...?
>>
>> All the best,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
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Received on Wed Feb 26 2014 - 12:30:02 PST
