[gmx-users] secondary structure analyze

[Parisa Rahmani]

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 "
>> 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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