[gmx-users] MARTINI / all-atom mapping

[Michael Daily]

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.periole at 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)
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-- 
====================================
Michael D. Daily
Postdoctoral research associate
Pacific Northwest National Lab (PNNL)
509-375-4581
(formerly Qiang Cui group, University of Wisconsin-Madison)
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