Thanks Jason. I am able to handle it now..
On Thu, Nov 29, 2012 at 6:22 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Thu, Nov 29, 2012 at 6:46 AM, Ravi Tripathi <abhi.rt8687.gmail.com
> >wrote:
>
> > Dear amber users,
> > Is it possible to solvate the system with any solvent other than water
> > using Leap.
>
>
> Yes. But if the solvent is not available, you will need to create a
> solvent box unit. For instance, Amber provides an 8M urea solvent box (of
> course it is still aqueous, but it's not pure water). There is also a
> methyl-chloride box available, methyl alcohol, and an N-methyl acetamide
> box available (look in the $AMBERHOME/dat/leap/lib folder).
>
> and is it possible to fix number of solvent molecules during
> > solvation.
> >
>
> No. You can, however, adjust the buffer size to get as close as possible
> to the desired number of solvent molecules and then use parmed.py (or
> xparmed.py) to strip off the extras that you don't want.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> 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 Fri Nov 30 2012 - 02:30:02 PST
