<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><BR><DIV><DIV>30 mar 2007 kl. 22.40 skrev özge kül:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV>Hi Andrea,</DIV> <DIV> </DIV> <DIV>This is my .top file</DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">more 1ppbfree.top<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">;<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">;<SPAN style="mso-spacerun: yes"> </SPAN>File '1ppbfree.top' was generated<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">;<SPAN style="mso-spacerun: yes"> </SPAN>By user: ozge (502)<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">;<SPAN style="mso-spacerun: yes"> </SPAN>On host: druggrid<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">;<SPAN style="mso-spacerun: yes"> </SPAN>At date: Thu Mar 15 23:17:25 2007<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">;<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">;<SPAN style="mso-spacerun: yes"> </SPAN>This is your topology file<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">;<SPAN style="mso-spacerun: yes"> </SPAN>ALPHA-THROMBIN (E.C.3.4.21.5) COMPLEX W<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">;<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">; Include forcefield parameters<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">#include "ffG43a1.itp"<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><O:P><FONT face="Times New Roman" size="3"> </FONT></O:P></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">; Include chain topologies<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">#include "1ppbfree_H.itp"<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">#include "1ppbfree_L.itp"</FONT></FONT></DIV></BLOCKQUOTE>Have you looked in these included files?<BR><BLOCKQUOTE type="cite"><DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman"><O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><O:P><FONT face="Times New Roman" size="3"> </FONT></O:P></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">; Include water topology<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">#include "spc.itp"<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><O:P><FONT face="Times New Roman" size="3"> </FONT></O:P></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">#ifdef POSRES_WATER<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">; Position restraint for each water oxygen<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">[ position_restraints ]<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">;<SPAN style="mso-spacerun: yes"> </SPAN>i funct<SPAN style="mso-spacerun: yes"> </SPAN>fcx<SPAN style="mso-spacerun: yes"> </SPAN>fcy<SPAN style="mso-spacerun: yes"> </SPAN>fcz<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman"><SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1<SPAN style="mso-spacerun: yes"> </SPAN>1000<SPAN style="mso-spacerun: yes"> </SPAN>1000<SPAN style="mso-spacerun: yes"> </SPAN>1000<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">#endif<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><O:P><FONT face="Times New Roman" size="3"> </FONT></O:P></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">; Include generic topology for ions<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">#include "ions.itp"<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><O:P><FONT face="Times New Roman" size="3"> </FONT></O:P></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">[ system ]<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">; Name<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">ALPHA-THROMBIN (E.C.3.4.21.5) COMPLEX W in water<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><O:P><FONT face="Times New Roman" size="3"> </FONT></O:P></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">[ molecules ]<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">; Compound<SPAN style="mso-spacerun: yes"> </SPAN>#mols<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">Protein_H<SPAN style="mso-spacerun: yes"> </SPAN>1<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT size="3"><FONT face="Times New Roman">Protein_L<SPAN style="mso-spacerun: yes"> </SPAN>1<O:P></O:P></FONT></FONT></DIV> <DIV class="MsoNormal" style="MARGIN: 0cm 0cm 0pt"><FONT face="Times New Roman" size="3">SOL<SPAN style="mso-spacerun: yes"> </SPAN>8695</FONT></DIV> <DIV> </DIV> <DIV> </DIV> <DIV>Thank you very much again and again...</DIV><DIV> <BR class="khtml-block-placeholder"></DIV><HR size="1">No need to miss a message. <A href="http://us.rd.yahoo.com/evt=43910/*http://mobile.yahoo.com/mail">Get email on-the-go </A><BR>with Yahoo! Mail for Mobile. <A href="http://us.rd.yahoo.com/evt=43910/*http://mobile.yahoo.com/mail">Get started.</A><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">_______________________________________________</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">gmx-users mailing list<SPAN class="Apple-converted-space"> </SPAN><A href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please search the archive at <A href="http://www.gromacs.org/search">http://www.gromacs.org/search</A> before posting!</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Please don't post (un)subscribe requests to the list. Use the<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">www interface or send it to <A href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</A>.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Can't post? Read <A href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</A></DIV> </BLOCKQUOTE></DIV><BR><DIV> <SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><SPAN class="Apple-style-span" style="border-collapse: separate; border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-align: auto; -khtml-text-decorations-in-effect: none; text-indent: 0px; -apple-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><BLOCKQUOTE type="cite"></BLOCKQUOTE><DIV>_______________________________________________</DIV><DIV>Erik Marklund, PhD student</DIV><DIV>Laboratory of Molecular Biophysics,</DIV><DIV>Dept. of Cell and Molecular Biology, Uppsala University.</DIV><DIV>Husargatan 3, Box 596,<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>75124 Uppsala, Sweden</DIV><DIV>phone:<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>+46 18 471 4537<SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>fax: +46 18 511 755</DIV><DIV><A href="mailto:erikm@xray.bmc.uu.se">erikm@xray.bmc.uu.se</A><SPAN class="Apple-tab-span" style="white-space:pre"><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "><SPAN class="Apple-style-span" style="white-space: pre; "> </SPAN></SPAN></SPAN></SPAN>http://xray.bmc.uu.se/molbiophys</DIV><BR class="Apple-interchange-newline"></SPAN></SPAN></SPAN></SPAN> </DIV><BR></BODY></HTML>