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 <[EMAIL PROTECTED]> 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/[EMAIL >> PROTECTED]/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 >> > >> > >> > >> >======================================== >> > >> >> > >> >> >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to [EMAIL PROTECTED] >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > -- > ======================================== > > 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 > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
