Re: AMBER: about antechamber

From: David A. Case <>
Date: Mon, 11 Oct 2004 09:13:05 -0700

On Sat, Oct 09, 2004, MURAT CETINKAYA wrote:
> I have a non standard residue (GFP chromophore) that I should build with
> antechamber. If I try gaff parameters, I get the prepin file but head and
> tail atoms are not the ones I want (I get an O atom instead of N and some
> side chain C atom instead of the backbone C atom). So, I cannot build my
> protein using this residue and other standard resiues.

There is a detailed example of creating an amino-acid like residue (with the
proper head and tail atoms, etc). in the "examples" page of the antechamber
web site (which in turn you reach from the Amber web site):

....hope this helps....dac

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Received on Mon Oct 11 2004 - 17:53:01 PDT
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