<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><SPAN class="Apple-style-span">These problems are typically due to grompp not finding cpp (make sure it's in your path) or having opened the top file in some non-linux text editor. Open the top file in vi and see if you see '<B>M^</B>' where you would expect line breaks. If so your top file is polluted. To change from mac line breaks to unix use:</SPAN><DIV><BR class="khtml-block-placeholder"></DIV><DIV><SPAN class="Apple-style-span"></SPAN>tr '\015' '\012' <bad.top> fixed.top</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV><DIV>Where '\015' is the mac line break and '\012' is the unix. If it's a windows prob. you'll have to google for the windows line break code. </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>I have had occasions where the above did not fix the solution, very frustrating. If nether of the above fix the problem just re-create your .mdp file in vi, this always fixes this problem.</DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Good luck, </DIV><DIV><BR class="khtml-block-placeholder"></DIV><DIV>Ken</DIV><DIV><SPAN class="Apple-style-span"><BR><DIV><DIV>On Dec 15, 2006, at 12:22 PM, David van der Spoel wrote:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Александр Журавлев wrote:</DIV> <BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">A problem with Gromacs-3.3: When I try ty run grompp using a.gro and a.top files, system says that number of coordinates in a.gro, 440, does not match number of coordinates in a.top, 0. That's strange because the both files were converted by pdb2gmx from one: a.pdb. Maybe it's necessary to specify number of atoms somewhere in a.top file?<SPAN class="Apple-converted-space"> </SPAN>_______________________________________________</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 don't post (un)subscribe requests to the list. Use the 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 style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">please check the output from pdb2gmx again, and also the top file. There is most likely an error there.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">--<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">David.</DIV><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; ">David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Dept. of Cell and Molecular Biology, Uppsala University.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Husargatan 3, Box 596,<SPAN class="Apple-converted-space"> <SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN></SPAN>75124 Uppsala, Sweden</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">phone:<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>46 18 471 4205<SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>fax: 46 18 511 755</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</A><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>spoel@gromacs.org <SPAN class="Apple-converted-space"> </SPAN>http://folding.bmc.uu.se</DIV><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; ">_______________________________________________</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 don't post (un)subscribe requests to the list. Use the</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></SPAN></DIV></DIV></BODY></HTML>