VMD-L Mailing List

From: Mauricio Carrillo Tripp (trippm_at_gmail.com)
Date: Wed Sep 21 2005 - 12:51:04 CDT

Yes, it would be nice to read GROMACS' ITP or TOP files directly with VMD.
I've tried to use 'top2psf' before with no luck. I wanted to convert the
topology
files from GROMACS because I needed to see a DCD trajectory produced by
NAMD using gromacs force filed, so I didn't have a PSF. I did notice though,
that when first loading the initial PDB coordinates I could load the DCD
with
no (apparent) problem. Of course, probably the reason this worked is because
I did have a (well behaved) PDB file in the first place.

On 9/21/05, John Stone <johns_at_ks.uiuc.edu> wrote:
>
>
> 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
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> 

--
Mauricio Carrillo Tripp, PhD
Department of Chemistry
Wabash College
trippm_at_wabash.edu
http://trippm.bajacast.com/