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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.<BR>
Thanks alot<BR>
<BR>
>Maybe I can help with some more details. I'm sorry if my explanation is<BR>
>to much detailed.<BR>
><BR>
>I start to use do_dssp a few days ago. I went to the website Justin just<BR>
>mentioned and I just downloaded the binary file. I copy that file to<BR>
>/usr/local/bin<BR>
>The binary file that I downloaded is dsspcmbi. So, before try do_dssp I<BR>
>create a soft link "dssp" to the binary dsspcmbi. I've created the link<BR>
>in the same directory (/usr/local/bin), and everything is just work fine.<BR>
><BR>
>Nuno Azoia<BR>
><BR>
><BR>
><BR>
>Justin A. Lemkul wrote:<BR>
> ><BR>
> ><BR>
> > minnale wrote:<BR>
> >><BR>
> >> Thanks for the reply Justin<BR>
> >> I tried like this<BR>
> >> do_dssp -f .xtc -s .tpr -n .ndx -map str.map -o str<BR>
> >> it has given<BR>
> >> Fatal error:<BR>
> >> DSSP executable (/usr/local/bin/dssp) does not exist (use setenv DSSP)<BR>
> >><BR>
> ><BR>
> > The prerequisite is a separate (non-Gromacs) program called DSSP. It<BR>
> > is available here:<BR>
> ><BR>
> > http://swift.cmbi.ru.nl/gv/dssp/<BR>
> ><BR>
> > Install dssp into /usr/local/bin and try do_dssp again.<BR>
> ><BR>
> > -Justin<BR>
> ><BR>
> >> I checked with archives do_dssp is a seperate program and install<BR>
> >> separately,<BR>
> >> Could you pls tell me how can I install do_dssp program or is there<BR>
> >> anyway to calculate secondary structure of protein?<BR>
> >> Thanks in advance.<BR>
> >><BR>
> >><BR>
> >> On Fri, 15 Aug 2008 Justin A.Lemkul wrote :<BR>
> >> ><BR>
> >> >As a final note, it is probably better to use the .xtc file for<BR>
> >> analysis. The do_dssp program is very slow, and I can only imagine<BR>
> >> that reading the full-precision trajectory will slow to an absolute<BR>
> >> crawl.<BR>
> >> ><BR>
> >> >-Justin<BR>
> >> ><BR>
> >> >Justin A. Lemkul wrote:<BR>
> >> >><BR>
> >> >><BR>
> >> >>minnale wrote:<BR>
> >> >>> Hi all,<BR>
> >> >>> I want to analyse secondary struture of my protein which have<BR>
> >> run MD for 7ns. I have checked in archives about do_dssp, found that<BR>
> >> can use only .pdb file instead of .trr and .tpr. Then if type command<BR>
> >> with -h it has it has given .xtc, .tpr, and .ndx should use.<BR>
> >> >><BR>
> >> >>Where does it say that you can't use your trajectory? That's<BR>
> >> certainly incorrect. The standalone dssp program (which you must<BR>
> >> obtain separately from the DSSP site) can only run on a single .pdb<BR>
> >> file, but Gromacs makes use of the dssp executable such that it can<BR>
> >> be used with trajectories.<BR>
> >> >><BR>
> >> >>Hence the lovely plots you see in the literature.<BR>
> >> >><BR>
> >> >>-Justin<BR>
> >> >><BR>
> >> >>>I am bit confusing with about do_dssp command.<BR>
> >> >>>Can you explain me clearly. Thanks in advance.<BR>
> >> >>><BR>
> >> >>><BR>
> >> >>><BR>
> >> >>>Rediff Shopping<BR>
> >> <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><BR>
> >><BR>
> >><BR>
> >> ><BR>
> >> >Justin A. Lemkul<BR>
> >> >Graduate Research Assistant<BR>
> >> >Department of Biochemistry<BR>
> >> >Virginia Tech<BR>
> >> >Blacksburg, VA<BR>
> >> >jalemkul[at]vt.edu | (540) 231-9080<BR>
> >> >http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<BR>
> >> ><BR>
> >> >========================================<BR>
> >><BR>
> >><BR>
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