From: Nathan C. Rockwell (ncrockwell_at_ucdavis.edu)
Date: Wed Sep 21 2005 - 14:17:10 CDT

I'm another gromacs user! Although my only complaint on importing gromacs
stuff is that working with the .gro and .trr (structure and trajectory,
respectively) I haven't figured out how to avoid getting a duplicate frame
from importing the trr, which is pretty close to the bottom of my list of
things to do, much less anybody else's.

In looking at the original message, I noticed a couple of questions about
this specific case:
1. is this GROMOS or gromacs? They're not the same thing; gromacs just uses
GROMOS force fields, among others.
2. gromacs (and maybe GROMOS) uses nm and not Angstroms as distance, so
that's a frequent source of confusion when people try their own scripts.
3. at least on the mac, there are newline problems that confuse VMD if you
use a word processor (as opposed to a text editor)--these typically manifest
as weird bonding and missing atoms, etc.

nr

On 9/21/05 8:20 AM, "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.
>>