VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 21 2005 - 10:20:02 CDT

Hi,
  I looked at the Gromacs web site and it would seem that the ".dat" files
aren't a documented format at all. It's hard for me to say why your
conversion program doesn't work right, but if your main problem is that
you're getting incorrect bonding and such, this is probably simply an issue
of VMD being forced to guess bonds by a distance based bond search since
it isn't getting that information from your PDB file. The Gromacs web page
only had this to say about these .dat files:
  http://www.gromacs.org/documentation/reference_3.2/online/dat.html

If you have the structure in a normal Gromacs topology file, it would
probably be pretty easy to write a new Gromacs topology file reader
plugin that retrieves the correct bonding information and without having to
convert to a PDB file. If there are other Gromacs users on the VMD-L list
that would like to see VMD read more of the Gromacs files directly without
conversion, speak up now. What files do you guys want to be able to read?
If nobody wants new reader plugins I have plenty of other things to work on,
but this could probably be done in a day or two if there is sufficient demand.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 21, 2005 at 10:37:35AM -0400, Stanley Lan wrote:
> Hi everyone,
>
> >From Gromos output I got ***sxmd.dat (final coordinates) and ***rxmd1.dat,
> along with the topology file(***mta.dat). I tried to convert the final
> coordinates into pdb format and import it into VMD. It worked except the
> whole molecule is in pieces(broken bonds, mis-connected bonds). Same thing
> happend to other two visualization programs, PyMol and RasMol. I assumed
> it's because the final coordinats from GROMOS doensn't have the standard
> amino acid residues and the correct connection map. My boss didn't think
> so. He thinks there is something wrong with my conversion program and/or
> VMD.
>
> I try to prove he is wrong but I need to be able to import the gromos
> output files into VMD without conversion. Any comments/suggestions will be
> appreciated.
>
> Is there any GROMOS archive with string search function for me to search
> this kind of questions/answers?
>
> Ben.
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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