AMBER Archive (2009)

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

From: case (case_at_biomaps.rutgers.edu)
Date: Tue Nov 03 2009 - 05:30:07 CST

On Tue, Nov 03, 2009, nicholus bhattacharjee wrote:

> 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.

Amber does not implement a constant-pH method using explicit solvent.

...dac

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