AMBER Archive (2007)

Subject: RE: AMBER: missing impropers for nitros?

From: Junmei Wang (jwang_at_encysive.com)
Date: Mon May 21 2007 - 12:48:58 CDT

Hi, David,
The main purpose of improper torsion parameters is to keep a planar
conformation for C=C, C=O etc. I think you may simply add X-o-no-o 1.1
180 2 to gaff.dat to avoid the warning.

All the 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, May 21, 2007 10:47 AM
To: Junmei Wang
Cc: amber_at_scripps.edu
Subject: Fwd: AMBER: missing impropers for nitros?

Dear Junmei,

Can I get your help here? I'm just trying to figure out if I need to be
deriving an improper torsion for gaff nitros, or if the warning is
ignorable, or...

Thanks,
David

---------- Forwarded message ----------
From: David Mobley <dmobley_at_gmail.com>
Date: May 11, 2007 5:03 PM
Subject: AMBER: missing impropers for nitros?
To: Junmei Wang <jwang_at_encysive.com>, amber_at_scripps.edu

Junmei and all,

I'm running ANTECHAMBER and LEAP to try and generate GAFF parameters for
a variety of small molecules, and I keep getting warnings about missing
improper torsions for pretty much everything with a nitro group (for
example, 1-nitrobutane gives me a warning about "No sp2 improper
torsion term for c3-o-no-o".

Can anyone shed some insight here? Why is there a nitro type but no
improper torsion for these?

Thanks,
David
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