[gmx-users] CG Mapping section for g_fg2cg

[Thomas Schmidt]

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
> >
> >
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