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<DIV>Hi,<BR>> <BR>> I have many problems embendding my protein in a bilayer.<BR>> <BR>> I used the package make hole with a POPE bilayer of 340 monolypids.<BR>> <BR>> The result is once i inserted my protein in, i can't even run an EM as <BR>> the result is bad.<BR>> <BR>> I also don't manage to download the manual. Don't know why i tried with <BR>> different system the connection never works.<BR>> <BR>> I wonder about how to calcul the area per lipid to check if this bilayer <BR>> was ok, is there a special way to do it?<BR>> <BR>> I also would like to know how to see the overlaps between my protein and <BR>> the lipid bilayer, i am not using rasmol, is it the only way?<BR>> <BR>> Something else: when i run the EM on my protein only, im vacuum, the <BR>> Maximum force is about 700 <BR></DIV>
<DIV>> I was using an amber force field, to get my model is it possible that =<BR>> the problem comes from the changement?</DIV>
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<DIV>and final question in the method to put the protein in a bilayer, how to positionnate the protein in regard to the membrane? I juste did it with translation and rotation the way i tought it was the best. Now I wonder it was not the way to do it.<BR>> <BR>> in advance thank you very much for your time.=20<BR>> <BR>> Audrey<BR>> <BR></DIV><BR><BR><BR>
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<DIV></DIV>Herr Audrey </FONT></STRONG>
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<DIV><STRONG><FONT face="Courier New, Courier, Monospace" color=#ff6633><FONT color=#3333cc>exchange student in Bioinformatics and modelling</FONT> </FONT></STRONG></DIV>
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<DIV><STRONG><FONT face="Courier New" color=#ff6633>0416 363 076</FONT></STRONG></DIV>
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<DIV><STRONG><FONT face="Courier New" color=#333399>University of Sydney 425 Harris St.</FONT></STRONG></DIV>
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<DIV><STRONG><FONT face="Courier New" color=#333399>physical chemestry Ultimo, Sydney 2007</FONT></STRONG></DIV>
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<DIV><STRONG><FONT face="Courier New" color=#333399>ou en France:</FONT></STRONG></DIV>
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<DIV><STRONG><FONT face="Courier New" color=#333399>6 alle des cytises</FONT></STRONG></DIV>
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<DIV><STRONG><FONT face="Courier New" color=#333399>71640 Dracy le Fort</FONT></STRONG></DIV>
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<DIV></DIV></div><br clear=all><hr> <a href="http://g.msn.com/8HMWFR/2015">Cliquez-ici</a> </html>