[gmx-users] How much does DSSP need to analyze lysozyme? => more than one hour

Chih-Ying Lin chihying2008 at gmail.com
Sun Jun 28 07:00:07 CEST 2009


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
  export PATH=$PATH:$DSSP

  Is it correct ?

Thank you

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