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

[Justin A. Lemkul]

Chih-Ying Lin wrote:
> 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'

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 
for analysis.

-Justin

> 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
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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