[gmx-users] do_dssp

[Justin A. Lemkul]

minnale wrote:
>  
> Thanks for the reply Justin
> I tried like this
> do_dssp -f .xtc -s .tpr -n .ndx -map str.map -o str
> it has given
> Fatal error:
> DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)
> 

The prerequisite is a separate (non-Gromacs) program called DSSP.  It is 
available here:

http://swift.cmbi.ru.nl/gv/dssp/

Install dssp into /usr/local/bin and try do_dssp again.

-Justin

> I checked with archives do_dssp is a seperate program and install 
> separately,
> Could you pls tell me how can I install do_dssp program or is there 
> anyway to calculate  secondary structure of protein?
> Thanks in advance.
> 
> 
> On Fri, 15 Aug 2008 Justin A.Lemkul wrote :
>  >
>  >As a final note, it is probably better to use the .xtc file for 
> analysis.  The do_dssp program is very slow, and I can only imagine that 
> reading the full-precision trajectory will slow to an absolute crawl.
>  >
>  >-Justin
>  >
>  >Justin A. Lemkul wrote:
>  >>
>  >>
>  >>minnale wrote:
>  >>>  Hi all,
>  >>>  I want to analyse secondary struture of my protein which have run 
> MD for 7ns. I have checked in archives about do_dssp, found that can use 
> only .pdb file instead of .trr and .tpr. Then if type command with -h it 
> has it has given .xtc, .tpr,  and .ndx should use.
>  >>
>  >>Where does it say that you can't use your trajectory?  That's 
> certainly incorrect.  The standalone dssp program (which you must obtain 
> separately from the DSSP site) can only run on a single .pdb file, but 
> Gromacs makes use of the dssp executable such that it can be used with 
> trajectories.
>  >>
>  >>Hence the lovely plots you see in the literature.
>  >>
>  >>-Justin
>  >>
>  >>>I am bit confusing with about do_dssp command.
>  >>>Can you explain me clearly. Thanks in advance.
>  >>>
>  >>>
>  >>>
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>  >-- ========================================
>  >
>  >Justin A. Lemkul
>  >Graduate Research Assistant
>  >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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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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