[gmx-users] secondary structure analyze
jalemkul at vt.edu
Tue Jan 1 20:09:20 CET 2013
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/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 A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
More information about the gromacs.org_gmx-users