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

[Justin A. Lemkul]

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

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