[gmx-users] DSSP hangs for days

sharada sharada at ccmb.res.in
Sun Jun 28 10:46:24 CEST 2009

 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.
-- Original Message --
From: Chih-Ying Lin <chihying2008 at gmail.com>
To: gmx-users at 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
type =>
do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc
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
=> 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
Is it correct ?
Thank you
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