AMBER Archive (2002)

Subject: FWD: RE: Including explicit waters in GB dynamics

From: Kristina Furse (kristina.e.furse_at_vanderbilt.edu)
Date: Fri Aug 02 2002 - 15:32:52 CDT

Had a request for the response I got to this question, so if anyone else is
interested, here it is! (Thanks dac!)

>===== Original Message From David Case <case_at_scripps.edu> =====
On Sat, Jul 20, 2002, Kristina Furse wrote:
>
> I am running some dynamics on a crystal structure using generalized Born to
> approximate solvent, but would like to include a few explicit
crystallographic
> water molecules that are somewhat buried and appear to be interacting with
the
> protein in interesting ways. I was wondering if AMBER GB is calibrated for
> this type of hybrid continuum/explicit water calculations? Any advice?

It's not particularly "calibrated" for this purpose, but what you suggest
ought to work OK. If they are buried waters, they will probably stay put
for reasonable length simulations, but there is nothing in particular that
otherwise would keep them near the starting positions.

..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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****************************************************
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
email: kfurse_at_structbio.vanderbilt.edu