AMBER Archive (2007)

Subject: AMBER: Improper angle by Antechamber

From: Pavan G (pavanamber_at_gmail.com)
Date: Sun Jan 28 2007 - 11:28:29 CST

Hello all,

I am trying to parameterize a drug and I used antechamber to obtain the
prepin file. The code found three improper angles [pictures attached. In
JPEG format and virus-free]. How do I ensure that these are the only three
improper angles in the system? Why can't atoms C19-C21-C18-C20 or
C20-C15-C24-C19 form an improper angle? I understand that improper angles
confine geometry and sometimes determine the chirality of the central atom.

Thank you.

Pavan


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