Re: AMBER: Amber8: problem related to antechamber

From: David A. Case <>
Date: Mon, 16 Oct 2006 08:29:19 -0700

On Mon, Oct 16, 2006, priya priya wrote:
> When I use antechamber to load a peptoid sequence
> (peptoids have the amino acid side chain appended to
> amide nitrogen ratther then alpha carbon) containing
> charged residues (like lysine). it says "ODD NUMBER OF
> ELECTRONS"....Check!
> There are three lysine residues and the total number of electrons come out
> to be 834 but antechamber is taking 837 number of electrons (not
> considering the +3 charge of the three lysine residues.

You have to explicitly tell antechamber the net charge using the "-nc" flag.
The default is zero.

Note also that antehcamber is designed to handle a *single* residue at a time,
not multiple residules as you seem to be trying.

...good luck...dac

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Received on Wed Oct 18 2006 - 06:07:16 PDT
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