[gmx-users] MARTINI / all-atom mapping

[Thomas Piggot]

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.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)

-- 
Dr Thomas Piggot
University of Southampton, UK.

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