<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;">Dear Nada,</SPAN></FONT></FONT><DIV><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;"><BR class="khtml-block-placeholder"></SPAN></FONT></FONT></DIV><DIV class="MsoNormal"><SPAN style=""><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;">In order to run the script please use</SPAN></FONT></FONT><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;"><FONT class="Apple-style-span" color="#000000"></FONT></SPAN></FONT></SPAN></DIV><DIV class="MsoNormal"><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;"><BR class="khtml-block-placeholder"></SPAN></FONT></FONT></DIV><DIV class="MsoNormal"><SPAN style=""><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;">perl ../perl_files/make_hole.pl -f dmpc_npat.pdb -o outbilayer.pdb -r 1 -lipat P -lipid DMP</SPAN></FONT></FONT><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;"><O:P></O:P></SPAN></FONT></FONT></SPAN></DIV><DIV class="MsoNormal"><SPAN style="font-size:10.0pt;color:blue"><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;"> </SPAN></FONT></FONT><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;"><O:P></O:P></SPAN></FONT></FONT></SPAN></DIV><DIV class="MsoNormal"><SPAN style="font-size:10.0pt"><SPAN style="mso-tab-count: 1"><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;"> </SPAN></FONT></FONT></SPAN><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;">–f is the input file </SPAN></FONT></FONT><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;"><O:P></O:P></SPAN></FONT></FONT></SPAN></DIV><DIV class="MsoNormal"><SPAN style="font-size:10.0pt"><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;">–o is the output file</SPAN></FONT></FONT><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;"><O:P></O:P></SPAN></FONT></FONT></SPAN></DIV><DIV class="MsoNormal"><SPAN style="font-size:10.0pt"><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;">–r is the radius of the hole </SPAN></FONT></FONT><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;"><O:P></O:P></SPAN></FONT></FONT></SPAN></DIV><SPAN style="font-size:10.0pt;font-family:"Times New Roman";mso-ansi-language: EN-US;mso-fareast-language:EN-US"><FONT class="Apple-style-span" color="#000000"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;">–lipat is the molecule which determines if the dmpc molecule should be removed</SPAN></FONT></FONT></SPAN><DIV><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;"><BR class="khtml-block-placeholder"></SPAN></FONT></DIV><DIV><SPAN style="font-size:10.0pt;font-family:"Times New Roman";mso-ansi-language: EN-US;mso-fareast-language:EN-US"><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;"><FONT class="Apple-style-span" color="#000000"></FONT></SPAN></FONT></SPAN><FONT class="Apple-style-span" face="Didot" size="5"><SPAN class="Apple-style-span" style="font-size: 18px;">Good luck, Itamar.</SPAN></FONT><DIV><BR><DIV><DIV>On Jan 11, 2006, at 4:23 PM, nada taib wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV id="RTEContent"> dear professor<BR> <BR> <PRE><I>I would try to perform MD of protein inserted in a popc<BR> lipid bilayer but i' don't know how to make hole in popc <BR>and how to work with make-hole.pl<BR> </I><I>I will really</I> <I>appreciate</I><SPAN style="font-style: italic;"></SPAN><I> if you can help me<BR><BR>think you<BR></I></PRE> Nada TAIB<BR> Institut Européen de Chimie et de Biologie (IECB)<BR> CNRS UMR 5144 Molécules, Biomolécules et Objets Supramoléculaires (MoBIOS)<BR> 2, rue Robert Escarpit - 33607 Pessac Cedex - France<BR> Tél. : 33 (0)5 40 00 30 31<BR> Fax. : 33 (0)5 40 00 30 73<BR> <A href="http://www.iecb.u-bordeaux.fr">http://www.iecb.u-bordeaux.fr</A><BR> _____________________________ <BR> <BR> <BR> <BR> <BR> </DIV><DIV> <BR class="khtml-block-placeholder"></DIV><HR size="1"> Nouveau : téléphonez moins cher avec Yahoo! 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