Dear amber users,
Thanks a lot. Is there any way to restrict the number of
solvent molecules that I want to add in the box?.
Thanks in advance
Aneesh
On Thu, Mar 5, 2009 at 3:35 AM, Gustavo Seabra <gustavo.seabra.gmail.com>wrote:
> Hi,
>
> 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 <aneeshcna.gmail.com> 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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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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Received on Fri Mar 06 2009 - 01:17:40 PST
