Re: [AMBER] docking evaluation using amber

From: David Case <>
Date: Fri, 11 Mar 2011 21:18:26 -0500

On Mar 11, 2011, at 8:33 PM, erik zuiderweg <> wrote:

> We have docked a ligand to a protein using AUTODOCK 4.2.
> We use a protein structure that is minimized and equilibrated to 300K in Amber.
> AUTODOCK gives many docks that are structurally very different but "energetically" the similar.
> We want to evaluate the results using Amber 11.

Erik: I know I have been really bad about getting in touch with you. I don't have an "obvious" answer (which is one reason I delayed my reply--not a good excuse). I'll try to call on Monday, but we will probably need to get some sample inputs in order to see what is going on. Good news is that I have a post-doc working on docking and scoring who can probably help and you won't have to depend so much on me.


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Received on Fri Mar 11 2011 - 18:30:03 PST
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