On Thu, Sep 20, 2012 at 3:24 PM, <davide.savy.unina.it> wrote:
> Hello everyone!
> I am a new user at the very beginning. I need to create a box with 20
> sodium benozate molecules (I have already created the mol2 file in
> xleap). Now, I need to solvate them with 190 water molecules: how can
> I do that?
>
LEaP can only add solvent according to a 'buffer' size that describes how
far away from the solute the solvent is placed.
For instance:
solvateBox <system> <solvent> 15.0
will place as many solvent molecules as is necessary to make sure that
there is a solvent molecule at least 15 Angstroms away from every atom in
every direction. There's no way to calculate exactly how large a box must
be to get a specific number of molecules.
However, what you can do is try different buffer sizes until you get as
close to the number of water molecules that you want (but make sure you
have a couple more than you need rather than a couple fewer). Then, you
can use parmed.py (or xparmed.py) to remove the extra water molecules that
you don't want.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 20 2012 - 13:00:03 PDT
