AMBER Archive (2006)

Subject: AMBER: RE: antechamber bond typing questions

From: Junmei Wang (jwang_at_encysive.com)
Date: Mon Aug 07 2006 - 20:43:05 CDT

Hi, David,
There are six options of "-j" to do atom/bond type assignments. Just
type "antechamber -h " to get those options. If you have some problem
with bond type assignment, you may manually do corrections and then run
antechamber again to just assign atom types (-j 1).

Certainly, I can help you to figure out why the programs fail if you
provide us the problematic molecules.

Best

Junmei

==================================================
Dr. Junmei Wang
Chemistry & Biophysics
Encysive Pharmaceuticals Inc.
7000 Fannin, Houston TX 77030
Tel: 713-578-6649
Email: jwang_at_encysive.com
http://amber.scripps.edu/antechamber/antechamber.html
==================================================

-----Original Message-----
From: David Mobley [mailto:dmobley_at_gmail.com]
Sent: Monday, August 07, 2006 3:15 PM
To: David A. Case; Junmei Wang
Cc: amber_at_scripps.edu
Subject: antechamber bond typing questions

Dear Dr. Case and Dr. Wang,

I'm using antechamber to do atom/bond typing for some ligands from the
pdb, which I have protonated correctly, and in several particular cases
I'm not getting the correct bond/atom types (i.e., rings are being
assigned to be aromatic which should not be).

I can of course provide input files if you're interested in looking in
to this, but I was wondering if you could also help me with
work-arounds.

In particular, if, for example, I use antechamber to generate a mol2
file, and then manually edit the bond types and feed it back into
antechamber again, if I use a suitable -j option, is there a way to get
it to judge only the atom types again, and use the bond types I have
manually provided? Or is there a way to edit one of the
ANTECHAMBER_* files to correct the bond/atom type assignment?

If not, do you have any other suggestions on how to work around this?

Thanks,
David
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