AMBER Archive (2006)

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

From: Ross Walker (
Date: Mon Oct 16 2006 - 10:32:20 CDT

See the "-nc" command line option for antechamber.
E.g. (The following should work. Although you should check the QM output
carefully to be sure)

antechamber -i g98.out -fi gout -o sustiva_resp.mol2 -fo mol2 -c resp -nc 3

All the best


|\oss Walker

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From: [] On Behalf Of
priya priya
Sent: Monday, October 16, 2006 00:01
Subject: AMBER: Amber8: problem related to antechamber

Dear All

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

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.

Please suggest how to make the prepin file of such charged residues..

Priya Anand


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