[gmx-users] How much does DSSP need to analyze lysozyme? => more than one hour
Justin A. Lemkul
jalemkul at vt.edu
Sun Jun 28 19:34:35 CEST 2009
Chih-Ying Lin wrote:
> type =>
> do_dssp -f 6LYZ-MD.xtc -s 6LYZ-MD.tpr -o secondary-structure.xpm -sc
> Select a group: 1
> Selected 1: 'Protein'
Don't analyze Protein. Think about it - you're looking at mainchain hydrogen
bonds. Side chains and such don't matter for DSSP. Use the MainChain+H group
> 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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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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