VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Aug 24 2006 - 00:44:22 CDT

Hi,
  Here's the only .gro file format spec I can find presently:
http://www.gromacs.org/documentation/reference/online/gro.html

My understanding of that specification is that while the last 6
of the 9 box vectors may be omitted, the first three may not.
If I understand correclty, this means that files that are
completely missing the box vectors are illegally formatted.
Perhaps a Gromacs developer or expert could comment on this?

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 24, 2006 at 12:59:52AM -0400, Axel Kohlmeyer wrote:
>
> 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. 

-- 
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