Re: dynamics with different pH conditions

From: David Case <>
Date: Thu 23 Nov 2000 12:02:46 -0800

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

...good luck..dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
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Received on Thu Nov 23 2000 - 12:02:46 PST
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