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
--
==================================================================
David A. Case | e-mail: case_at_scripps.edu
Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
The Scripps Research Institute | phone: +1-858-784-9768
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La Jolla CA 92037 USA | http://www.scripps.edu/case
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Received on Thu Nov 23 2000 - 12:02:46 PST
