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
--
========================================
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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