AMBER Archive (2004)

Subject: AMBER: dummy atom other than H

From: Carsten Detering (
Date: Tue May 11 2004 - 20:12:22 CDT

Dear ambers,

how do I proceed if I want to open a ring for thermodynamic integration? I
have an isoindole ring, and I would like to make a C in the 5-ring an H, and
bind this H to the atom next to it. How can I tell sander to bind the
resulting H to one side, and remove the bond to the other? In smiles it
would look something like [nH]1cc2ccccc2c1 -> NC=C1=CC=CC=C1.

Thanks for helpful suggestions,


Carsten Detering
University of Washington
Department of Chemistry
Seattle, WA 98195
Fon 206.543.5081
Fax 206.685.8665

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