Hi, I waited for it to finish for almost 5 days nothing happened except creation of those files. I had posted a similar mail some time back. Is there no solution for this. Is it something to do with speed of the system? I ran the program on HP dual core system. sharada -- Original Message -- From: Chih-Ying Lin <chihying2...@gmail.com> To: gmx-users@gromacs.org Date: Sat, 27 Jun 2009 22:00:07 -0700 Subject: [gmx-users] How much does DSSP need to analyze lysozyme? => more than one hour HI 1. type => do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc secondary-structure.xvg Select a group: 1 Selected 1: 'Protein' There are 129 residues in your selected group Opening library file /usr/local/gromacs/share/gromacs/top/ss.map Reading frame 0 time 0.000 Back Off! I just backed up dd6S1IAF to ./#dd6S1IAF.1# dd0JIeYC dd2n5lZ5 dd6Lt1VG ddCKhtbw ddH0Kx1A ddH1OHJw ddH7I7Jq ddHu6YEP .......... etc are created........ => DSSP has been taking one hour to analyze the lysozyme and not finish yet => there may something wrong ??? 2. The path of the DSSP file is /usr/local/bin/DSSP. Both dsspcmbi and dsspcmbi.exe are in the file /usr/local/bin/DSSP. 3. So, the last step i type the command in my .profile. setenv dssp /usr/local/bin/DSSP export dssp= /usr/local/bin/DSSP export PATH=$PATH:$DSSP Is it correct ? Thank you Lin _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
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