<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY>Hi,<br > 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.<br ><br >sharada <font size="2" face="Arial"><TABLE STYLE="BORDER-BOTTOM-COLOR: blue; BORDER-LEFT: blue 1px solid; BORDER-TOP-COLOR: blue; PADDING-LEFT: 5px; BORDER-RIGHT-COLOR: blue"><tbody><TR><TD><br ><strong><em>-- Original Message --</em></strong><br >From: Chih-Ying Lin <chihying2008@gmail.com><br >To: gmx-users@gromacs.org<br >Date: Sat, 27 Jun 2009 22:00:07 -0700<br >Subject: [gmx-users] How much does DSSP need to analyze lysozyme? => more<br >than one hour<br ><br >HI<br ><br >1.<br >type =><br >do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc<br >secondary-structure.xvg<br ><br >Select a group: 1<br >Selected 1: 'Protein'<br >There are 129 residues in your selected group<br >Opening library file /usr/local/gromacs/share/gromacs/top/ss.map<br >Reading frame 0 time 0.000<br >Back Off! I just backed up dd6S1IAF to ./#dd6S1IAF.1#<br ><br ><br >dd0JIeYC dd2n5lZ5 dd6Lt1VG ddCKhtbw ddH0Kx1A<br >ddH1OHJw ddH7I7Jq ddHu6YEP<br >.......... etc are created........<br ><br >=> DSSP has been taking one hour to analyze the lysozyme and not finish<br >yet<br >=> there may something wrong ???<br ><br ><br ><br ><br >2. The path of the DSSP file is /usr/local/bin/DSSP.<br >Both dsspcmbi and dsspcmbi.exe are in the file /usr/local/bin/DSSP.<br ><br ><br >3. So, the last step i type the command in my .profile.<br >setenv dssp /usr/local/bin/DSSP<br >export dssp= /usr/local/bin/DSSP<br >export PATH=$PATH:$DSSP<br ><br >Is it correct ?<br ><br ><br >Thank you<br >Lin<br >_______________________________________________<br >gmx-users mailing list gmx-users@gromacs.org<br >http://lists.gromacs.org/mailman/listinfo/gmx-users<br >Please search the archive at http://www.gromacs.org/search before posting!<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 ></TD></TR></tbody></TABLE></font></BODY></HTML>