Asymmetric water molecule found???

From: Elsa F. Sousa Henriques (
Date: Wed May 03 2006 - 02:59:26 CDT


I'm trying to impose an artificial bond between a dummy atom and a
hydroxyl oxygen in my molecule, but I get the following error from namd:

> Charm++ fatal error:
> FATAL ERROR: Asymmetric water molecule found??? This can't be right.

It looks like the problem lies in the fact that my oxygen is (also)
bonded to a hydrogen, because if I impose such an artificial bond
between my dummy and another oxygen without any hydrogen bonded to it,
the program runs fine.

At first I though the 'rigidBonds' set to 'all' had something to do
with it so I set it to 'water' only, but the problem remains.

Any idea on how to go around this? Any suggestion would be greatly


P.S.: I am running NAMD 2.6b1 for Linux-i686

Elsa Henriques, Ph.D.
Frankfurt Institute for Advanced Studies   Tel: +49 (0)69 798 47502
Max von Laue Str. 1, room 1.215            Fax: +49 (0)69 798 47611
60438 Frankfurt am Main, Germany        E-mail:
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