Re: [AMBER] antechamber cannot match patching atoms of amino acid

From: David A Case <>
Date: Thu, 11 Aug 2016 08:05:53 -0400

On Wed, Aug 10, 2016, Chitrak Gupta wrote:
> I am trying to parameterize a novel amino acid, to be used as a part of a
> peptide.
> I tried using antechamber, but the program could not match the patching
> atoms. Is antechamber only for organic molecules, i.e. should I be using
> something else for parameterizine amino acids? Or is there a way to get
> anterchamber to match the patching atoms?

The procedure for using antechamber to parameterize a modified amino acid
(intended to be a part of a peptide) is different from that used for molecules
that are not covalently linked to something else. See tutorial B5 for an
walk-through of creating modified amino acids.

If you have trouble, please try to provide details: I don't recognize
the phrase "could not match the patching atoms".


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Received on Thu Aug 11 2016 - 05:30:03 PDT
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