Re: AMBER: solvate shell

From: David A. Case <>
Date: Thu, 15 Mar 2007 12:36:04 -0700

On Thu, Mar 15, 2007, janavi raghavan wrote:
> I am trying to solvate a protein with one layer of
> water.does the solvate shell command in amber perform
> the above operation .does solvateshell need the use of
> non-periodic boundary condition?if so then how do i
> include a code in the input file to restrain the
> surface water molecules only so that it does not
> evaporate.

See the "water cap" section of the manual (p. 99 for Amber 9). This is not
really for a single solvent shell, however. And please bear in mind Prof.
Simmerling's warnings that you will have to work hard to ensure that you are
getting a physically reasonable simulation. Amber serves as a research tool
(allowing new methods to be tried out), but running with a small solvent shell
(while possible) has not yet received careful attention. So study the
literature carefully!


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Received on Sun Mar 18 2007 - 06:07:23 PDT
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