[gmx-users] secondary structure analyze
rahmani.prs2 at gmail.com
Tue Jan 1 20:17:39 CET 2013
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.
On Tue, Jan 1, 2013 at 10:39 PM, Justin Lemkul <jalemkul at 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 "
>> 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/**
>> 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 A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
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