Date: Thu, 23 Nov 2000 12:02:46 -0800
From: David Case
Subject: Re: dynamics with different pH conditions

On Thu, Nov 23, 2000, Ramasamy Thilagavathi wrote:

> Can I do dynamic simulations with pH conditions. If yes, how I can perform?

There is no such facility in Amber (or in other programs I am familiar
with). Each amino acid side chain must be assigned a unique (and constant)
protonation state. Of course these assignments themselves could be based on
pH, but there is no facility to have a partially protonated site.

Some development work is going on in these directions, but don't hold your
breath.

...good luck..dac