[gmx-users] MARTINI / all-atom mapping

[Justin A. Lemkul]

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/jp071097f

I 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

> Mike
> 
> On Tue, Aug 30, 2011 at 3:06 AM, XAvier Periole <x.periole at rug.nl 
> <mailto:x.periole at 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)
>>     -- 
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> 
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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)
> 

-- 
========================================

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

========================================