Hi Justin, Thanks for the expedient reply. So in that case I cannot get the dssp output of my CG structure for sure. So in that case do I have to get the .ssd files of my 1K4C_clean.pdb file only right and then get the .seq file of 1K4c_clean.pdb in order to proceed. Am I right?
Sunny On Tue, Aug 18, 2009 at 1:03 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > sunny mishra wrote: > >> Dear all, >> >> I wanted to get the dssp output of Coarse Grained structure of my protein >> i.e. 1K4C. In order to get that I have a script which is given to me in the >> MARTINI tutorial (dssp2ssd.py). I have also downloaded the dssp successfully >> in my linux machine. In my first step i cleaned the 1K4C protein and renamed >> it as 1K4C_clean.pdb. 1K4C_clean.pdb consists only the header title and >> atoms with C ligands in it. When i convert the 1K4C_clean.pdb to CG >> structure using atom2CG script with the help of awk command I get the CG >> structure successfully and I renamed it 1K4C_cleancg.pdb. But when I am >> trying to get the dssp output of 1K4C_cleancg.pdb using dssp it produces >> nothing but on the other hand it produces the dssp output of my normal >> cleaned 1K4C pdb file. Do you know if there is anyway I can get the dssp >> output of my CG structure of protein? >> >> > Not likely. DSSP calculates secondary structure from hydrogen bonds, which > will be absent in a CG model. The script you refer to (dssp2ssd.py) does > not use DSSP to calculate secondary structure; it simply converts DSSP > output to the .ssd file needed by MARTINI. > > -Justin > > Thanks, >> >> Sunny >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > 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://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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