Re: Asymmetric water molecule found

From: Peter Freddolino (
Date: Tue May 12 2009 - 06:45:32 CDT

Hi Jorgen,
you're running afoul of some safety checks in the namd code, associated
with setting up rigidbonds if I recall correctly. You might instead want
to use extraBonds (available in namd 2.7b1) to add the bond to the metal
ion instead of having it in the molecule topology.

Jorgen Simonsen wrote:
> Hi all,
> I get this error and see that others have had it before me but couldn't
> find any solution to it. I have modified a water molecule and added a
> bond between it and a metal ion and changed the charge of it as well - I
> have look into vmd and the bond and geometries look fine
> Any hints or suggestion appreciated
> thanks in advance
> Best
> Jorgen

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