[gmx-users] secondary structure analyze

[Justin Lemkul]

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 <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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-- 
========================================

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

========================================