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

Thomas Schmidt schmidt at bit.uni-bonn.de
Tue Oct 20 13:51:07 CEST 2009

Dear Nicholas,

I've needed a bit time for testing but this works fine.
Many thanks for that script.


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

On Mo, 2009-10-19 at 16:53 +0200, Nicolas Sapay wrote:
> Hello Thomas,
> I have a tcl script in my personal script library that might do what you 
> want to do. I didn't use it for quite a while, but it was working well 
> as far as I remember. I think it has been adapted from a script 
> available on the VMD website, but I don't remember exactly its history. 
> It doesn't seem too difficult to understand. You should be able to 
> modify it for your own purpose, if needed.
> Cheers,
> Nicolas
> Thomas Schmidt a écrit :
> > 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

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