Dear David, <br><br>I tried to use x2top, but it ended up with the following error:<br><br> 0: GROMOS96 43a1 force field <br> 1: GROMOS96 43b1 vacuum force field<br> 2: GROMOS96 43a2 force field (improved alkane dihedrals)<br> 3: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)<br> 4: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656) <br> 5: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656) <br> 6: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)<br> 7: [DEPRECATED] Gromacs force field (see manual)<br> 8: [DEPRECATED] Gromacs force field with hydrogens for NMR<br> 9: Encad all-atom force field, using scaled-down vacuum charges<br>10: Encad all-atom force field, using full solvent charges <br>0<br>Looking whether force field file ffG43a1.rtp exists<br>Opening library file /share/apps/gromacs-3.3/share/gromacs/top/ffG43a1.rtp<br>Generating bonds from distances...<br>Opening library file
/share/apps/gromacs-3.3/share/gromacs/top/ffG43a1.atp<br>There are 49 type to mass translations<br>atom 438<br>-------------------------------------------------------<br>Program x2top, VERSION 3.3<br>Source code file: futil.c, line: 537<br><br>Fatal error:<br>Library file ffG43a1.n2t not found in current dir nor in default directories.<br>(You can set the directories to search with the GMXLIB path variable)<br><br>Could you tell me what is wrong? Many thanks!!!<br><br>Cherry<br><br><br><b><i>David van der Spoel <spoel@xray.bmc.uu.se></i></b> wrote:<blockquote class="replbq" style="border-left: 2px solid rgb(16, 16, 255); margin-left: 5px; padding-left: 5px;"> Cherry Y. Yates wrote:<br>> Dear gromacs developers and users,<br>> <br>> I am calculating a nanotube which has periodic boundary condition along <br>> one direction. I wonder how to make an itp file for this system. The <br>> difficulty lies in describing the bond between two end atoms, e.g., two
<br>> atoms are bonded in an infinite length system, but are located on the <br>> bottom and top of a unit cell.<br>use x2top<br>and in your mdp file use pbc=full<br><br>> <br>> Thanks,<br>> <br>> Cherry<br>> <br>> ------------------------------------------------------------------------<br>> Get your email and more, right on the new Yahoo.com <br>> <http: //us.rd.yahoo.com/evt="42973/*http://www.yahoo.com/preview"><br>> <br>> <br>> ------------------------------------------------------------------------<br>> <br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br><br>--
<br>David.<br>________________________________________________________________________<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755<br>spoel@xray.bmc.uu.se spoel@gromacs.org http://folding.bmc.uu.se<br>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<br>_______________________________________________<br>gmx-users mailing list gmx-users@gromacs.org<br>http://www.gromacs.org/mailman/listinfo/gmx-users<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-users-request@gromacs.org.<br>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br></http:></blockquote><br><p> 
<hr size=1>Yahoo! Messenger with Voice. <a href="http://us.rd.yahoo.com/mail_us/taglines/postman1/*http://us.rd.yahoo.com/evt=39663/*http://voice.yahoo.com">Make PC-to-Phone Calls</a> to the US (and 30+ countries) for 2¢/min or less.