Try looking at the programs VOIDOO (looks for cavities) and FLOOD
(floods the cavities with solvent).
Best wishes
Shozeb
Daniel Smith wrote:
> Hello,
>
> I am currently running Amber 9 but also have access to Amber 10 if need be.
> I have a channel protein that I am trying to simulate in vacuo. However, I
> would like to solvate the interior of the channel. How might I go about
> doing this other than placing the waters in there individually? I have tried
> solvating the protein, but that gives me thousands of unnecessary waters.
>
> Thank you,
> Daniel Smith
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Received on Fri Feb 13 2009 - 01:09:02 PST
