AMBER Archive (2009)

Subject: Re: [AMBER] Solvating the interior of a channel

From: Shozeb Haider (shozeb.haider_at_pharmacy.ac.uk)
Date: Wed Feb 11 2009 - 07:15:07 CST

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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