On May 11, 2012, at 8:32 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Hi Jason,
>
> I'm attaching the input file as per your request. I think you will recognise it (http://jswails.wikidot.com/ph-replica-exchange).
Ah, pH remd is not part of Amber 12. I added it to sander shortly after 12 was released (it's actually not even in the main developer branch yet, although it will be soon).
I will probably post a pure constant pH MD tutorial sometime this summer somewhere on either ambermd.org or my wiki.
Thanks!
Jason
>
> Best regards
>
> George
>
>
>
> On May 11, 2012, at 2:29 PM, Jason Swails wrote:
>
>> The problem is in your input file, so it would help if you attached that instead.
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>>
>> On May 11, 2012, at 5:30 AM, George Tzotzos <gtzotzos.me.com> wrote:
>>
>>> I'm trying to minimise the structure of a protein-ligand complex for constant pH simulations.
>>>
>>> Running: mpirun -np 12 sander.MPI -O -i min.in -o min.out -p complex.prmtop -c complex.inpcrd -r min.rst -ref complex.inpcrd
>>>
>>> gives the following error message:
>>>
>>> "At line 1019 of file _mdread.f (unit = 5, file = 'min.in')
>>> Fortran runtime error: End of file
>>> APPLICATION TERMINATED WITH THE EXIT STRING: Hangup (signal 1)"
>>>
>>> I'm attaching the md.out file hoping that someone could help me to sort out this problem.
>>>
>>> Best regards
>>>
>>> George
>>>
>>> <min.out>
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>>
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Received on Fri May 11 2012 - 06:00:05 PDT
