AMBER Archive (2009)

Subject: [AMBER] Solvating the interior of a channel

From: Daniel Smith (
Date: Tue Feb 10 2009 - 14:42:09 CST


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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