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Hi Mike,<br>
<br>
If you download the rev_trans.tar.gz archive from the reverse
transformation tutorial on the Martini website
(<a class="moz-txt-link-freetext" href="http://md.chem.rug.nl/cgmartini/index.php/tutorial/reverse-transformation">http://md.chem.rug.nl/cgmartini/index.php/tutorial/reverse-transformation</a>)
the mapping section at the end of the dppc.itp file provides the
details of the mapping for this lipid.<br>
<br>
Cheers<br>
<br>
Tom<br>
<br>
On 30/08/11 18:57, Michael Daily wrote:
<blockquote
cite="mid:CAF-wSYFxpd6mRc-Qr1y+nQwenEE4ZQZNEykHWOcBdt6ZoW6r4w@mail.gmail.com"
type="cite">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 moz-do-not-send="true"
href="mailto:x.periole@rug.nl">x.periole@rug.nl</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt
0.8ex; border-left: 1px solid rgb(204, 204, 204);
padding-left: 1ex;">
<div style="word-wrap: break-word;">
<div><br>
</div>
it must be some example of mapping lipids on the website:
<a moz-do-not-send="true" href="http://cgmartini.nl"
target="_blank">cgmartini.nl</a>
<div><br>
<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 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 moz-do-not-send="true"
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>
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</div>
<br>
<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>
509-375-4581<br>
(formerly Qiang Cui group, University of Wisconsin-Madison)</font></font><br>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Dr Thomas Piggot
University of Southampton, UK.
</pre>
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