VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Wed Aug 23 2006 - 23:59:52 CDT

On Wed, 23 Aug 2006, Marc Charendoff wrote:

marc,

please see my reply to your previous mail.

http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/7605.html

your .gro file is not conformant to the .gro sprecifications
(or at least according to what whoever wrote the gromacs
plugin thought they were). just add the correct box dimensions
(or some arbitrary numbers at the end of the file, and it
will work.

unfortunately, there is no easy way to make the gromacs plugin
more forgiving for this kind of omission, since that would
kill the support for .gro format trajectories in turn.

cheers,
  axel.

MC> Hello,
MC>
MC> I'm still trying to visualize a *.gro file made by the
MC> PRODRG server. When I load the molecule I get this:
MC>
MC> Info) Using plugin gro for structure file
MC> /Users/Marc/Desktop/BDEXxtrct.GRO
MC> Warning, error reading box, unexpected end-of-file
MC> reached
MC>
MC> Any hints or guidance on what to do?
MC>
MC> Thanks, Marc
MC> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.