Dear Xavier, well, sorry. I was on the wrong way. :-) I'm trying to map a model from the atomistic scale into CG. All the time I searched for a possibility to define atoms to CG-Beads. I was confused because of the awk script "atom2cg" which simply puts out only a couple of atom types that were not defined in the MARTINI ff. But I didn't recognize that I already have a valid topology from "seq2itp", which is runing very well, and don't need anything more.
Anyway, many thanks for your answer and time. 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 Mo, 2009-10-26 at 15:17 +0100, XAvier Periole wrote: > It is not clear what you actually want to do! > > 1- You want to generate a topology for MARTINI: follow > the tutorial, which I believe is clear. > > 2- you want to play with the reverse transformation. For a > protein I believe that there is a parameter file that contains > the CG-AA mapping. For other molecules you have to do it > your self by hand, following examples given in the workshop > would be the best ... > > On Oct 26, 2009, at 2:13 PM, Thomas Schmidt wrote: > > > Dear all, > > > > how can I create the mapping section for "g_fg2cg" in the atomistic > > *.itp file? The handout from the Coarse Graining Workshop 2009 says > > that > > pdb2gmx has this ability but I can't find it: > > http://www.csc.fi/english/research/sciences/chemistry/courses/cg-2009/CGWS_Tutorial.pdf/download > > > > . > > > > By running pdb2gmx of both, GROMACS version 4 and the reverse-mapping > > GROMACS (including g_fg2cg), I didn't get any result similar to this > > mapping section in my output files. > > > > Maybe now there's also another way to setup a CG model for the MARTINI > > force field. (?) > > > > Many thanks for your answers. > > > > Nice greetings, > > 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 [email protected] > > 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 [email protected]. > > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
