[gmx-users] CG Mapping section for g_fg2cg
schmidt at bit.uni-bonn.de
Mon Oct 26 16:14:48 CET 2009
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 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, 2009-10-26 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
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