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)
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> >>> >>> >>>------------------------------------------------------------------------ >>> >>>_______________________________________________ >>>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 > >========================================
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