AMBER Archive (2009)

Subject: Re: [AMBER] Some queries about pH simulation

From: nicholus bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Tue Nov 03 2009 - 01:34:02 CST

Sorry to disturb you people again. I just want to do a simulation of protein
a different pH values. A similar problem is done the following paper

Molecular dynamics simulations of the native
and partially folded states of ubiquitin: Influence
of methanol cosolvent, pH, and temperature
on the protein structure and dynamics
Protein Science (2007), 16:1101–1118

The pH simulation in the above paper is done by GROMOS96. Can the problem be
done with AMBER. In short I want to simulate my protein in explicit solvent
at different different pH values. What should I do? Please help.

On Sat, Oct 10, 2009 at 12:07 AM, nicholus bhattacharjee <
nicholusbhattacharjee_at_gmail.com> wrote:

> Thanx a lot dear Jason and Carlos.
> 

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