Specbond.dat is used to construct the topology, Ozge. so it is used by pdb2gmx program. Alpay
Message: 6 Date: Sat, 31 Mar 2007 00:36:14 +0200 From: Erik Marklund <[EMAIL PROTECTED]> Subject: Re: [gmx-users] splitting chains To: Discussion list for GROMACS users <gmx-users@gromacs.org> Message-ID: <[EMAIL PROTECTED]> Content-Type: text/plain; charset="iso-8859-1" 30 mar 2007 kl. 22.32 skrev özge kül:
Hi Eric, Where is the specbond.dat?After which line is it formed?
specbond.dat is located in <install directory>/share/gromacs/top/ I don't understand the question about the line. /Erik
1. pdb2gmx_mpi -f 1ppbfree.pdb -p 1ppbfree.top -o 1ppbfree.gro -merge 2.editconf_mpi -f 1ppbfree.gro -o -d 0.8 -bt octahedron 3. genbox_mpi -cp out.gro -cs -p 1ppbfree.top -o 1ppbfree-gen.gro 4. grompp_mpi -v -f 1ppbfree-en.mdp -c 1ppbfree-gen.gro -o 1ppbfree-en.tpr -p 1ppbfree.top 5.mdrun_mpi -v -s 1ppbfree-en.tpr -o 1ppbfree-en.trr -c 1ppbfree- aftermin.gro -g 1ppbfree-en.log -e 1ppbfree-en.edr Please help me?:) özge Bored stiff? Loosen up... Download and play hundreds of games for free on Yahoo! Games. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________ Erik Marklund, PhD student Laboratory of Molecular Biophysics, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: +46 18 471 4537 fax: +46 18 511 755 [EMAIL PROTECTED] http://xray.bmc.uu.se/molbiophys -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20070331/d17b33c5/attachment.html ------------------------------ _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 35, Issue 99 ***************************************** _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
