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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