AMBER Archive (2009)

Subject: Re: [AMBER] Regarding leap

From: Gustavo Seabra (
Date: Wed Mar 04 2009 - 16:05:25 CST


If you read the manual carefully, you will notice that both solvatebox
and solvateoct commads have a similar syntax:

> solvateBox solute solvent distance [ closeness ]
> solvateOct solute solvent distance [ closeness ]

Here, just as the solute can be anything, so does the solvent. It is
not restricted to water. As long as you have your solvent defined in
LEaP, you can use it as the "solvent" argument.

Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA

On Wed, Mar 4, 2009 at 6:43 AM, aneesh cna <> wrote:
> Dear amber users,
>                I am using amber 9.0 for simulation. I would like to add
> some organic molecules in a cubic box  by keeping my protein of interest at
> the center of box,  just like what 'solvetbox' command doing in leap with
> water molecules.But instead of water I would like to add organic molecules.
> Can anyone suggest me how to do this in amber?
> Thanks in advance
> Aneesh
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