[gmx-users] MARTINI / all-atom mapping

[XAvier Periole]

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.piggot at 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.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)
> 
> -- 
> Dr Thomas Piggot
> University of Southampton, UK.
> -- 
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