[gmx-users] secondary structure analyze

[Justin Lemkul]

On 1/1/13 2:06 PM, Parisa Rahmani wrote:
> Hi gmx users
>
> I want to do secondary structure analyze for my trajectory of protein.
> I've downloaded DSSP packages from "
> ftp://ftp.cmbi.ru.nl/pub/software/dssp/dssp-2.0.4.tgz"
> and put it in /usr/local/bin , and rename the folder to dssp.
> when i run "do_dssp -f rmsd.pdb -s protein.tpr -sc scount.xvg -o ss.xpm"
>
> the following appears,
>
> Opening library file /home/parisa/parisa/share/gromacs/top/phbres.dat
> Opening library file /home/parisa/parisa/share/gromacs/top/aminoacids.dat
> Group     0 (      System) has   420 elements
> Group     1 (     Protein) has   420 elements
> Group     2 (   Protein-H) has   322 elements
> Group     3 (     C-alpha) has    43 elements
> Group     4 (    Backbone) has   128 elements
> Group     5 (   MainChain) has   171 elements
> Group     6 (MainChain+Cb) has   208 elements
> Group     7 ( MainChain+H) has   214 elements
> Group     8 (   SideChain) has   206 elements
> Group     9 ( SideChain-H) has   150 elements
> Select a group: 1
> Selected 1: 'Protein'
> There are 43 residues in your selected group
> Opening library file /home/parisa/parisa/share/gromacs/top/ss.map
> Reading frame       0 time    1.000
> Back Off! I just backed up dd35REJx to ./#dd35REJx.1#
>
>
> and the program is continuously running without .xpm and xvg outputs.
>
>
> i searched the mailing list, but I couldn't find  the solution (because
> many of them was about the old DSSP version , that is not available now)
>
> any suggestion would be greatly appreciated.
>

do_dssp is very slow.  The output files are only produced at the very end, when 
the program is done running.  For some of my longer trajectories, the program 
runs for a few hours.  It all depends on how many frames you have to analyze.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
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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