Xavier, I did find the atom2cg.awk script on the downloads-> tools of the martini website, but there is no corresponding one for lipids. In any case I can probably figure out the mapping by trial and error, just based on inter-bead distances, but it would be nice to have it officially documented.
Mike On Tue, Aug 30, 2011 at 3:06 AM, XAvier Periole <x.peri...@rug.nl> wrote: > > it must be some example of mapping lipids on the website: cgmartini.nl > > On Aug 30, 2011, at 3:55 AM, Michael Daily wrote: > > Hi all, > > I am trying to reverse-map some martini lipids to united atom. In order to > do this, I'd prefer to have an EXACT definition of the aa-to-cg mapping. I > cannot find this, only an imprecise graphic, in the MARTINI paper; the > martini.itp file doesn't appear to list which heavy atoms are represented by > each CG bead either. For example, I'm looking for something like: > > 'NC3' : ['C1', 'C2', 'C3', 'N4', 'C5', 'C6'], > 'PO4' : ['O7', 'P8', 'O9', 'O10', 'O11','C12'], > 'GL1' : ['C13', 'O14', 'C15', 'O16'], > 'GL2' : ['C32', 'O33', 'C34', 'O35'], > > etc. > > For some atoms it's obvious which MARTINI groups they belong in, but others > on the borderline are not obvious. For example, does C12 belong in PO4 or > GL1? > > Anybody have a master list like this? > > Thanks, > Mike > > -- > ==================================== > Michael D. Daily > Postdoctoral research associate > Pacific Northwest National Lab (PNNL) > 509-375-4581 > (formerly Qiang Cui group, University of Wisconsin-Madison) > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- ==================================== Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison)
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists