On 1/1/13 2:17 PM, Parisa Rahmani wrote:
Thanks Justin for the reply,
how i can sure that it uses the DSSP package correctly ,
it seems that it just uses the gromacs code :
(
Opening library file /home/parisa/parisa/share/gromacs/top/phbres.dat
Opening library file /home/parisa/parisa/share/gromacs/top/aminoacids.dat
Opening library file /home/parisa/parisa/share/**gromacs/top/ss.map
)
for some reasons I use gromacs 3.3.3.
The do_dssp program is simply a wrapper that runs the (external) dssp executable
on every frame in the trajectory. Gromacs has several definitions it uses for
various properties of the different residues, so that's what you see it opening.
If there are no errors, it is running correctly. Failures are rather obvious by
design.
-Justin
On Tue, Jan 1, 2013 at 10:39 PM, Justin Lemkul <jalem...@vt.edu> wrote:
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<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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/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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