From: Chris Harrison (charris5_at_gmail.com)
Date: Wed Nov 03 2010 - 06:02:40 CDT
This happens in two situations; both involve rigid bond algorithms and
water. You probably have rigid bonds on and a severally distorted water
structure. Try turning off rigid bonds, performing a short equilibration
and then turning rigid bonds back on.
On Wed, Nov 3, 2010 at 5:03 AM, Jérôme Hénin <jhenin_at_ifr88.cnrs-mrs.fr>wrote:
> 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 <Stefan_Franzen_at_ncsu.edu> 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
-- Chris Harrison, Ph.D. Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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