AMBER Archive (2005)

Subject: RE: AMBER: gaff atom types

From: Junmei Wang (jwang_at_encysive.com)
Date: Tue Apr 19 2005 - 11:18:44 CDT

Hi, Claudio,
Yes, cyano group is not considered as electron withdrawing group in
gaff. Only N, O, F, Cl, Br that directly bonded to the carbon to which
the hydrogen(s) is bonded are considered electron withdrawing groups.

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
==================================================

Subject: AMBER: gaff atom types

Dear Amber users,
 
When preparing a prepi file for CH3(CN), antechamber assigned hc type to
the hydrogen atoms. I was expecting to get h1 type for these hydrogens
(hydrogen on aliphatic carbon with 1 electron withdrawing group). Does
that mean that the cyano group is not considered as electron withdrawing
group when attached to an aliphatic carbon?
 
Any help you could give me would be greatly appreciated.
 
Claudio
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