Thank you Marc, this is a useful suggestion.
George
On May 11, 2012, at 3:13 PM, Marc van der Kamp wrote:
> Hi,
>
>
>> "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"
>>
>
> Why not determine what the protonation states of your residues would be at
> pH=4.0 and run standard MD (not constant pH MD), at least as an initial
> test.
> Presumably, many of the histidines would be doubly protonated, and perhaps
> some glutamate / aspartates as well.
>
> --Marc
>
>
>>
>> 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 - 06:30:05 PDT
