AMBER: creating a new residue

From: Amber admin <>
Date: Mon, 28 Feb 2005 08:44:59 -0800

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From: Kara Di Giorgio
Subject: I need Help creating a residue
Date: Fri, 25 Feb 2005 12:22:34 -0800

I have a DNA binding drug that I'm trying to model with a 10-mer DNA
strand. I've created a guanine with my compound bound to it.. I have
gotten this to run through antechamber to assign charges, atom types,
etc. I can't seem to format it correctly as a residue. (It needed to
be a complete molecule to use antechamber.)

I can open it in xLeap and manually delete the extra atoms and set the
head and tail, but now the overall molecular charge is wrong.

I've tried to use prepgen, but I obviously don't understand it as I
can't get it to work. (Even after viewing the tutorials)

Has anyone done this type of thing? Any help would be a godsend.

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Received on Mon Feb 28 2005 - 16:53:01 PST
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