Jason,
Thanks. Actually I'm using Amber 11 and my intention is NOT to run REMD. I do not want to titrate any of the ionisable residues.
I want to run a traditional MD simulation at pH=4.0
The protein I'm dealing with has "lid" over the binding cavity which is assumed to open at acidic pH releasing the bound ligand.
All I want to do is test this assumption. Isn't the constant pH method suitable for this?
Best regards
George
On May 11, 2012, at 2:40 PM, Jason Swails wrote:
>
>
> 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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Received on Fri May 11 2012 - 06:30:03 PDT
