Michael Daily wrote:
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.
One of the MARTINI papers describes some of the mapping: dx.doi.org/10.1021/jp071097fI don't think there's a table for each lipid available anywhere, but that paper should give some impression of how things are connected, at least for a few simple lipids.
-Justin
MikeOn Tue, Aug 30, 2011 at 3:06 AM, XAvier Periole <x.peri...@rug.nl <mailto:x.peri...@rug.nl>> wrote:it must be some example of mapping lipids on the website: cgmartini.nl <http://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 <tel:509-375-4581> (formerly Qiang Cui group, University of Wisconsin-Madison)-- gmx-users mailing list gmx-users@gromacs.org<mailto: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 <mailto:gmx-users-requ...@gromacs.org>. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists-- gmx-users mailing list gmx-users@gromacs.org <mailto: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 <mailto: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)
-- ======================================== Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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.
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