[gmx-users] Coarse-Grain: GROMACS bond information to VMD
schmidt at bit.uni-bonn.de
Mon Oct 19 16:20:06 CEST 2009
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
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 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
> 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
> files to VMD? Especially for coarse-grained models (using the
> 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
> 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
> or into the (NAMD) *.psf format. (?)
> The solution that I've found (top2psd.pl) is not smart enough
> 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 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
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