[gmx-users] CG Mapping section for g_fg2cg

XAvier Periole x.periole at rug.nl
Mon Oct 26 15:17:22 CET 2009

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    gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list