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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
