VMD-L Mailing List

From: Axel Kohlmeyer (axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de)
Date: Thu Sep 22 2005 - 07:32:55 CDT

On Wed, 21 Sep 2005, Stanley Lan wrote:

SL> Hi everyone,
SL>

hi,

SL> >From Gromos output I got ***sxmd.dat (final coordinates) and ***rxmd1.dat,
SL> along with the topology file(***mta.dat). I tried to convert the final
SL> coordinates into pdb format and import it into VMD. It worked except the
SL> whole molecule is in pieces(broken bonds, mis-connected bonds). Same thing

this is most likely due to parts of the molecule being wrapped back into
the unitcell during the MD because of periodic boundary conditions. if you
have enough solvent/vacuum around the molecule you might be able to 'fix'
this by shifting the whole system by half a box diagonal or so and then
apply PBC again.

SL> happend to other two visualization programs, PyMol and RasMol. I assumed
SL> it's because the final coordinats from GROMOS doensn't have the standard
SL> amino acid residues and the correct connection map. My boss didn't think
SL> so. He thinks there is something wrong with my conversion program and/or
SL> VMD.

i am attaching a converter for (formatted) gromos trajectories, that i
wrote some time ago. it will produce a .pdb and .dcd combo from the
gromos files. perhaps that'll work better for you. since it was written
for a specific system, you may have to augment it a little bit, though.

SL> I try to prove he is wrong but I need to be able to import the gromos output
SL> files into VMD without conversion. Any comments/suggestions will be
SL> appreciated.

you can try loading the files into VMD as type g96, but to the best of
my knowledge, not all record types (e.g. POSITIONRED) are supported.

regards,
        axel.

SL>
SL> Is there any GROMOS archive with string search function for me to search
SL> this kind of questions/answers?
SL>
SL> Ben.
SL>
SL>
SL> 

-- 
=======================================================================
Dr. Axel Kohlmeyer   e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
Lehrstuhl fuer Theoretische Chemie          Phone: ++49 (0)234/32-26673
Ruhr-Universitaet Bochum - NC 03/53         Fax:   ++49 (0)234/32-14045
D-44780 Bochum  http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.