On Thu, Sep 1, 2011 at 5:18 PM, Ismail, Mohd F. <farid.ou.edu> wrote:
> Hi,
>
> When one uses the solvateBox command, is there a way to control the number
> of solvent molecule created?
>
No. Here is what you can do: experiment with different sizes until you get
as close as possible to the number of solvent molecules you want, but make
sure that you have a few too many (rather than too few). Then, save the
system as a PDB file, then edit that PDB file and remove however many waters
you want removed.
Then load that PDB back into leap (with the correct number of waters), and
use the "setbox" command (find it in the AmberTools manual for how to use
it) to apply periodic boundary conditions.
HTH,
Jason
> --Farid
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 01 2011 - 19:00:02 PDT
