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. 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 > >> > > >> >======================================== > >> > >>
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