Thanks Justin and Thomas for the helpful comments. Thomas pointed to the example I had in mind. I should have been more specific.
It is obvious that we should make the mapping of molecules more easily accessible. Tks for the comments, XAvier. On Aug 30, 2011, at 20:16, Thomas Piggot <t.pig...@soton.ac.uk> wrote: > Hi Mike, > > If you download the rev_trans.tar.gz archive from the reverse transformation > tutorial on the Martini website > (http://md.chem.rug.nl/cgmartini/index.php/tutorial/reverse-transformation) > the mapping section at the end of the dppc.itp file provides the details of > the mapping for this lipid. > > Cheers > > Tom > > On 30/08/11 18:57, 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. >> >> 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) > > -- > Dr Thomas Piggot > University of Southampton, UK. > -- > 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
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