AMBER Archive (2006)

Subject: RE: AMBER: problem with prepfile

From: Junmei Wang (
Date: Thu May 25 2006 - 11:24:51 CDT

Dr. Chowdhury
In addition to Dave's suggestion, you may produce a new "residue" that
is made up of the steroid and the linked amino acid residue. The
procedure how to produce non-standard amino acid residues is
demonstrated by 4-hydroxyl-Proline. Please go to for details

Good luck


Sent: Wednesday, May 24, 2006 2:50 PM
Subject: AMBER: problem with prepfile

Dear AMBER users

I have a problem during the generation of the prepfile of the molecule I
would like to use. It is a steroid linked with a peptide.I tried many
ways but could not solve that problem. I enclosed mol2 file of the
molecule and prep file I got from ANTECHAMBER.

If anybody can help with this I will always appreciate that.

I am eagerly waiting for the reply.

With kind regards.

Shafinaz F. Chowdhury, PhD
Research Associate,
Computational Chemistry,
Biotechnology Research Institute,
National Research Council of Canada.
Tel: 514 496 6338
Fax: 514 496 5174
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