Dear Leila,
With the information you have provided, you might want to try PACKMOL -
http://www.ime.unicamp.br/~martinez/packmol/<
http://www.ime.unicamp.br/%7Emartinez/packmol/>
Starting with a pdb for a water molecule and the pdb of your solute, you can
easily define a PACKMOL input to prepare your system.
Regards,
Igor Marques
On Tue, Dec 7, 2010 at 3:21 PM, Oliver Grant <olivercgrant.gmail.com> wrote:
> in leap use this command:
>
> solvatebox <nameofyourstructure> TIP3PBOX 8.0
>
> Oliver
> On 7 December 2010 12:00, leila karami <karami.leila1.gmail.com> wrote:
>
> > Dear amber users
> >
> > I'm beginner in amber.
> >
> > I want to have a water box with following conditions:
> >
> > water model = TIP3P
> > distance between the solute and wall of the box = 8 angstroms
> > number of water molecules = 7400
> > box type = cubic
> > box length = 62 angstroms
> >
> > How I should use solvatebox for obtaining them?
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 07 2010 - 08:00:02 PST
