Dear Adrian,
I have gone through both the manual of Amber 9 as well
the test run. I have some confusions which I will mail you later. But before
that please tell is their any tutorial about the problem I am doing i.e.
simulating the protein at different different Phs. I am asking for type of
tutorial as can be found for say like simulating metalo proteins.
Thank you
Nicholus
On Sun, Aug 30, 2009 at 12:18 PM, Adrian Roitberg <roitberg.qtp.ufl.edu>wrote:
> $AMBERHOME/test/cnstph
>
> adrian
>
>
>
> nicholus bhattacharjee wrote:
>
>> Dear Adrian,
>> I am sorry for the mistake of writing temperature
>> instead of pH. I just want to simulate my protein in different different
>> pHs. Which test example should I follow? Thank you for the advice.
>>
>> On Sun, Aug 30, 2009 at 11:26 AM, Adrian Roitberg <roitberg.qtp.ufl.edu
>> >wrote:
>>
>> Dear Nicholus,
>>> I am confused about your post. You say you want to simulated it at
>>> different pHs and then ask how to regulate the temperature. These are two
>>> different questions.
>>>
>>> if you want to do constant pH, read the manual please and one of the
>>> tests
>>> examples under amber. It is not trivial to set up, but perfectly doable.
>>> For
>>> starters, you will need to recreate your prmtop with the protonable
>>> residues.
>>>
>>> Adrian
>>>
>>>
>>> nicholus bhattacharjee wrote:
>>>
>>> Dear community,
>>>> I am trying to simulate my protein in different
>>>> pH values. I am using Amber 9. Can anyone tell me how to regulate the
>>>> temperature. Thank you in advance.
>>>>
>>>>
>>>> --
>>> Dr. Adrian E. Roitberg
>>> Associate Professor
>>> Quantum Theory Project
>>> Department of Chemistry
>>>
>>> Senior Editor. Journal of Physical Chemistry
>>> American Chemical Society
>>>
>>> University of Florida PHONE 352 392-6972
>>> P.O. Box 118435 FAX 352 392-8722
>>> Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>
>>
>>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project
> Department of Chemistry
>
> Senior Editor. Journal of Physical Chemistry
> American Chemical Society
>
> University of Florida PHONE 352 392-6972
> P.O. Box 118435 FAX 352 392-8722
> Gainesville, FL 32611-8435 Email adrian.qtp.ufl.edu
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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Received on Wed Sep 02 2009 - 23:07:15 PDT
