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Hi,<br>
<br>
Perhaps you can do just like you did in pymol, but isntead of saving
the file, mearly write down the coordinates of the newborn water and
enter it into your gro-file.<br>
<br>
Cheers,<br>
<br>
Erik<br>
<br>
Adva Suez skrev 2010-12-01 08.59:
<blockquote
cite="mid:AANLkTimOPkE_sAzi6pJP5x44CrCGiPmEmQ5jjK46FdXZ@mail.gmail.com"
type="cite">
<div dir="ltr">Hello all!<br>
I would like to insert a molecule to a membrane system and would
like to start from a specific position of the molecule
(hydrocarbon or lipid headgroups). I tried doing that in Pymol
after converting the merged gro into pdb (using editconf) but
when I saved the file in Pymol the order of the lipids atoms got
mixed up and it does not match the dppc.itp anymore. Then it
caused problems in grompp.<br>
Do you have another way to set the position of the molecule in
the system? maybe without converting to PDB...??<br>
<br>
<br>
Thanks,<br>
Adva.<br clear="all">
<br>
-- <br>
<div dir="ltr"><font face="arial, helvetica, sans-serif">Adva
Yeheskel<br>
Bioinformatics Unit<br>
Rm 001, Sherman bldg.,<br>
G.S.W. Faculty of Life Sciences<br>
Tel-Aviv University, ISRAEL 69978 <br>
<br>
Tel: 972-3-6406840; Fax: 972-3-6405098<br>
E-mail: </font><a moz-do-not-send="true"
href="mailto:suezadva@tauex.tau.ac.il" target="_blank"><font
face="arial, helvetica, sans-serif">suezadva@tauex.tau.ac.il</font></a><font
face="arial, helvetica, sans-serif"><br>
Web-site: </font>
<div style="display: inline;"><span style="border-collapse:
collapse;"><a moz-do-not-send="true"
href="http://www.tau.ac.il/lifesci/bioinformatics.html"
style="color: rgb(28, 81, 168);" target="_blank"><font
face="arial, helvetica, sans-serif">http://www.tau.ac.il/lifesci/</font><font
face="arial, helvetica, sans-serif">bioinformatics.html</font></a></span></div>
</div>
<br>
</div>
</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 4537 fax: +46 18 511 755
<a class="moz-txt-link-abbreviated" href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</a> <a class="moz-txt-link-freetext" href="http://folding.bmc.uu.se/">http://folding.bmc.uu.se/</a>
</pre>
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