[gmx-users] Coarse-Grain: GROMACS bond information to VMD

[Thomas Schmidt]

Dear Omer,

many thanks for your answer, but your solution doesn't work for me.
We have Protein-Lipid models in the CG scale.
Only if I replace all atom names in the PDB file through "CA" I can use
the "trace" drawing method, but get also wrong atoms connected to each
other. For example CG Beads with low distances to each other, e.g. in
coarse-grained benzene rings, were not connected. I guess that this
method is distance dependent, too, but in another way. :-)

Does anybody else have a solution (...to put GROMACS bond information
into VMD)?

Thomas

-- 
Thomas H. Schmidt, PhD student
Computational Structural Biology
Chair of Life Science Informatics, B-IT
LIMES-Institute, University of Bonn
Dahlmannstrasse 2, D-53113 Bonn, Germany

Phone: +49-(0)228-2699 323
Fax: +49-(0)228-2699 341
http://www.csb.bit.uni-bonn.de



On Sa, 2009-10-17 at 18:16 +0200, Omer Markovitch wrote:
> What I do is visualize as trace. Than all the coarse-grained sphere
> are connected. Hope it helps. Omer.
>  
> Koby Levy research group,
> Weizmann Institute of Science. 
> FAX: 972-77-444-7905
> http://www.weizmann.ac.il/sb/faculty_pages/Levy/
> 
> 
> On Fri, Oct 16, 2009 at 11:24, Thomas Schmidt
> <schmidt at bit.uni-bonn.de> wrote:
>         Dear all,
>         
>         is there any possibility to give the bond information out of
>         GROMACS
>         files to VMD? Especially for coarse-grained models (using the
>         MARTINI
>         FF) this would be a nice feature for visualization.
>         
>         But in that case the distance analysis doesn't work, because
>         we will
>         always have too high distances between two particles (CG
>         scale). If I
>         use "Dynamic Bonds" (as described in this thread:
>         http://oldwww.gromacs.org/pipermail/gmx-users/2008-September/036124.html) VMD draws bonds also between non-bonded particles.
>         
>         I know that there is no official solutions for this
>         (http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD),
>         but maybe
>         anybody of you has a script to convert *.top/*.itp/*.rtp files
>         with a
>         corresponding *.gro file into the PDB format with connectivity
>         section
>         or into the (NAMD) *.psf format. (?)
>         The solution that I've found (top2psd.pl) is not smart enough
>         because
>         it's a simple 1-to-1 conversion of GROMACS topology files and
>         has not
>         the ability to replicate (and renumber) the topological data
>         of single
>         molecules (http://baaden.free.fr/soft/compchem.html).
>         
>         Thanks for your help...
>         Thomas
>         
>         --
>         Thomas H. Schmidt, PhD student
>         Computational Structural Biology
>         Chair of Life Science Informatics, B-IT
>         LIMES-Institute, University of Bonn
>         Dahlmannstrasse 2, D-53113 Bonn, Germany
>         
>         Phone: +49-(0)228-2699 323
>         Fax: +49-(0)228-2699 341
>         http://www.csb.bit.uni-bonn.de
>         
>         
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