VMD-L Mailing List

From: Stefan Franzen (Stefan_Franzen_at_ncsu.edu)
Date: Wed Nov 03 2010 - 02:11:22 CDT

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