Re: [AMBER] Changing pH of the system

From: Adrian Roitberg <roitberg.qtp.ufl.edu>
Date: Sun, 30 Aug 2009 16:26:01 +0100

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
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Received on Wed Sep 02 2009 - 23:06:22 PDT
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