OK. Thanks a lot justin On Tue, Aug 18, 2009 at 1:16 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > sunny mishra wrote: > >> 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? >> >> > Right, to generate the MARTINI topology you need both .ssd and .seq files. > > -Justin > > Sunny >> >> >> On Tue, Aug 18, 2009 at 1:03 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> 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 >> <mailto: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 >> <mailto: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 <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >
_______________________________________________ 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
