From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Sat Oct 02 2004 - 00:37:12 CDT
Hi Alberto,
You didn't check the hydrated psf file and pdb file together did you?
Did you make your cell basis vectors insanely large just as a check?
Are all energies 999999 or is it bond, or angles or torsions?
Can you post the psf,pdb files and a snippet of the log file showing the
energies?
Brian
On Fri, 1 Oct 2004, Alberto Santana wrote:
> Hi all,
>
> We are getting the Warning: "Not all atoms have unique coordinates" and
> energies like 99999999.9999. I checked the pdb file and all atoms have
> unique coordinates. Changing the cell basis vectors does not work either.
> Has NAMD gone mad???
>
> Funny, we get the warning if the system is hydrated, removing the water
> molecules makes the warning go away.
>
> Any ideas?
>
> -------------------------------------------------------------------
> Alberto Santana, Ph.D.
> Department of Chemistry
> University of Puerto Rico - Mayaguez
> P.O. Box 9019 Phone: (787) 832-4040 x3760
> Mayaguez PR, 00681-9019 http://www.uprm.edu/~asantana
>
>
*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:38:54 CST