[gmx-users] CG Mapping section for g_fg2cg

[XAvier Periole]

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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