AMBER Archive (2006)

Subject: Re: AMBER: Amber8: problem related to antechamber

From: David A. Case (
Date: Mon Oct 16 2006 - 10:29:19 CDT

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

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to