VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Jun 17 2008 - 09:11:03 CDT

On Mon, 16 Jun 2008, jake wernik wrote:

JW> I am trying to open a gromacs .gro file with my atomic coordinates
JW> but VMD gives the following message upon opening and does not
JW> display the molecule, only lists the number of atoms without bonds:

JW> Info) Using plugin gro for structure file E:/file.gro
JW> Warning, error reading box, unexpected end-of-file reached
JW> Info) Using plugin gro for coordinates from file E:/file.gro.
JW> Info) Finished with coordinate file E:/file.gro
JW> Info) Analyzing structure ...
JW> Info) etc....
JW>

JW> Can someone help explain what is wrong with the file format as I
JW> have loaded a similar .gro file before and it worked just fine. It
JW> seems that the program is very picky with the amount of characters
JW> or spaces used to define the parameters in the file.

it is really hard to tell what is going wrong without seeing
the offending file. also it would be nice to know what version
of VMD you are using (and perhaps gromacs, too). if you make
the file available, please make sure you gzip it first, so
that there are no CR-LF conversions happening, that may affect
the way how the file is parsed.

JW> Also, is there any resource available where I can read up on what
JW> the warning messages mean?

yep. the source code to the molfile plugins as contained in the
VMD source distribution.

cheers,
   axel.

JW>
JW> Thanks in advance.
JW>
JW> Mr. Wernik
JW> 

-- 
=======================================================================
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.