Re: Re: vmd-l: Asymmetric water molecule

From: Chris Harrison (charris5_at_gmail.com)
Date: Wed Nov 03 2010 - 06:02:40 CDT

Dear Stefan,

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.

Best,
Chris

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:
> http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/12228.html
>
> Best,
> Jerome
>
>
> 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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