AMBER Archive (2009)

Subject: Re: [AMBER] Changing pH of the system

From: nicholus bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Sun Aug 30 2009 - 10:40:42 CDT

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_at_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_at_qtp.ufl.edu
>
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> 

-- 
Nicholus Bhattacharjee
PhD Scholar
Department of Chemistry
University of Delhi
Delhi-110007 (INDIA)
Phone: 9873098743(M)
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