AMBER Archive (2009)

Subject: Re: [AMBER] Regarding leap

From: aneesh cna (aneeshcna_at_gmail.com)
Date: Wed Mar 04 2009 - 22:29:17 CST

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_at_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_at_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
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber