AMBER: Using Antechamber with Gamess and other molecular manipulations

From: Charles Karney <>
Date: Mon, 18 Jul 2005 13:28:20 -0400

Dear Colleagues:

I'd like to announce the availability of some scripts for manipulating
molecules written by researchers at Sarnoff Corporation under the
Engineered Identification and Countermeasures Program which is funded by
the U.S. Army Medical Research and Materiel Command under Contract
No. DAMD17-03-C-0082.

The main objectives of these scripts are

 * Allow Gamess to be used in conjunction with Antechamber for the
   assignment of partial charges by the RESP or AM1-BCC methods.
 * Add hydrogens to a PDB file using Gromacs and adjust atom names and
   certain bond angles to conform to Amber's rules.

A couple of shortcomings of Antechamber are addressed.

 * The charges produced by the AM1-BCC method are symmetrized between
   chemically equivalent atoms (using respgen's symmetry detection).
 * Antechamber produces several temporary files which mean that it is
   unsafe to run multiple instances within the same directory. This is
   addressed by placing the temporary files in a unique directory.

A full description of the scripts and the scripts themselves can be
found at

A backup site is

Questions, comments, and improvements on this work should be sent to

Charles Karney <>
Sarnoff Corporation, Princeton, NJ 08543-5300
Tel: +1 609 734 2312
Fax: +1 609 734 2323
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Received on Mon Jul 18 2005 - 20:53:01 PDT
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