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
Received on Thu Nov 29 2012 - 05:00:02 PST
