[gmx-users] Re: gmx-users Digest, Vol 52, Issue 66

[Tsjerk Wassenaar]

Please also note that *do_dssp* is part of the gromacs suite, and is
basically a wrapper around the third-party program *dssp* from CMBI,
calling it for every frame and processing the output. do_dssp relies
on the environment variable DSSP for locating dssp.

Tsjerk

On Mon, Aug 18, 2008 at 9:07 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> minnale wrote:
>>
>>
>> Thanks Nuno for your information , the archives mentioned website about
>>  do_dssp it's not freely available program. I couldnt able to get the
>> program, am I right Could please help me.
>
> Did you visit the website I linked in my earlier reply?  DSSP is indeed
> free. Visit the site, fill out the academic license, send it off, and
> download the software.  Which post says it's not free?
>
> -Justin
>
>> Thanks alot
>>
>>  >Maybe I can help with some more details. I'm sorry if my explanation is
>>  >to much detailed.
>>  >
>>  >I start to use do_dssp a few days ago. I went to the website Justin just
>>  >mentioned and I just downloaded the binary file. I copy that file to
>>  >/usr/local/bin
>>  >The binary file that I downloaded is dsspcmbi. So, before try do_dssp I
>>  >create a soft link "dssp" to the binary dsspcmbi. I've created the link
>>  >in the same directory (/usr/local/bin), and everything is just work
>> fine.
>>  >
>>  >Nuno Azoia
>>  >
>>  >
>>  >
>>  >Justin A. Lemkul wrote:
>>  > >
>>  > >
>>  > > 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.
>>  > >>  >>>
>>  > >>  >>>
>>  > >>  >>>
>>  > >>  >>>Rediff Shopping
>>  > >>
>> <http://adworks.rediff.com/cgi-bin/AdWorks/click.cgi/www.rediff.com/signature-default.htm/1050715198@Middle5/2206641_2199021/2201651/1?PARTNER=3&OAS_QUERY=null>
>>  > >>
>>  > >>
>>  > >>  >
>>  > >>  >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
>
> ========================================
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623