Xavier,<div><br></div><div>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.</div>
<div><br></div><div>Mike<br><br><div class="gmail_quote">On Tue, Aug 30, 2011 at 3:06 AM, XAvier Periole <span dir="ltr"><<a href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div style="word-wrap:break-word"><div><br></div>it must be some example of mapping lipids on the website: <a href="http://cgmartini.nl" target="_blank">cgmartini.nl</a><div><br><div><div><div></div><div class="h5"><div>On Aug 30, 2011, at 3:55 AM, Michael Daily wrote:</div>
<br></div></div><blockquote type="cite"><div><div></div><div class="h5">Hi all,<div><br></div><div>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:</div>
<div><br></div><div><div>'NC3' : ['C1', 'C2', 'C3', 'N4', 'C5', 'C6'],</div><div> 'PO4' : ['O7', 'P8', 'O9', 'O10', 'O11','C12'],</div>
<div> 'GL1' : ['C13', 'O14', 'C15', 'O16'],</div><div> 'GL2' : ['C32', 'O33', 'C34', 'O35'],</div></div><div><br></div><div>etc.</div>
<div> <br></div><div>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?</div><div><br></div><div>Anybody have a master list like this?</div>
<div><br></div><div>Thanks,</div><div>Mike<br clear="all"><div><br></div>-- <br><font><font size="2">====================================<br> Michael D. Daily<br> Postdoctoral research associate<br> Pacific Northwest National Lab (PNNL)<br>
<a href="tel:509-375-4581" value="+15093754581" target="_blank">509-375-4581</a><br> (formerly Qiang Cui group, University of Wisconsin-Madison)</font></font><br> </div></div></div> -- <br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
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509-375-4581<br>
(formerly Qiang Cui group, University of Wisconsin-Madison)</font></font><br>
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