Re: vmd-l: Asymmetric water molecule

From: Jérôme Hénin (
Date: Wed Nov 03 2010 - 05:03:40 CDT

Hi Stefan,

This is a NAMD question, so it belongs on the NAMD list: I am adding
it to the recipient list. Please remove the CC to VMD list in any
further replies.

You should find helpful information there:


On 3 November 2010 08:11, Stefan Franzen <> wrote:
> I am trying to model a heme with a bound water molecule.  The iron
> should be ferric iron, but this is a minor point.  I made a template
> for the topology file and added appropriate parameters for the Fe-O
> bond and Fe-O-H bending modes.  The error in the log file is
> "Asymmetric water molecule found??? This can't be right."
> I suspect that the program automatically checks waters in some way.  I
> can imagine that I may need to change the atom type to prevent this
> checking from recognizing this water, but it would really help if
> someone could tell me the origin of this error.
> Thank you very much.
> Stefan
> --
> Stefan Franzen
> Professor of Chemistry
> North Carolina State University
> Raleigh, NC 27695
> Phone: 919-515-8915

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