AMBER Archive (2000)

Subject: Re: dynamics with different pH conditions

From: David Case (case_at_scripps.edu)
Date: Thu Nov 23 2000 - 14:02:46 CST

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 

-- 

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David A. Case                     |  e-mail:      case_at_scripps.edu
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