Hi,
to my knowledge leap does not have this functionality (hopefully: yet).
You could try to generate a system with more water molecules, save it as
a pdb, delete the excess waters using an text editor like nedit or
emacs, and feed this modified pdb to leap again. This time without
adding water or ions. Do a *careful* pressure equilibration to take care
of box-size issues or density fluctuations.
hth,
simon
On 03.05.2012 13:33, Bala subramanian wrote:
> Friends,
> I am trying to create a solvent box with a particular number of water
> molecules (5800) around the protein. I have tried different buffer size
> around the protein so as to get the number of water molecules close to what
> i need and it resulted in 5798 water molecules. I would like to know if
> there is any way to add the extra two or three water molecules in leap or
> to delete extra water molecules from my system.
>
> Thanks,
> Bala
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Received on Thu May 03 2012 - 05:00:04 PDT
