Hi No i dont have any capping group shahid Nayeem
On 5/24/10, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > > shahid nayeem wrote: > >> Hi Justin >> I choose group 5 main chain for dssp calculation >> > > Do you have any capping groups (N-acetyl, C-amine, etc)? > > -Justin > > Shahid Nayeem >> >> >> On 5/24/10, *Justin A. Lemkul* <jalem...@vt.edu <mailto:jalem...@vt.edu>> >> wrote: >> >> >> >> shahid nayeem wrote: >> >> Dear All >> I did 10ns simulation of three peptide residue solvated in >> water. Each peptide residue is 26 residue long. In final .gro >> file it is showing total 78 residue which is O.K. as 3x26=78. >> For inserting three similar peptide I used genconf command. when >> I run dssp I get total residue as 80. The command for dssp is >> do_dssp -f .xtc -s .tpr -o ss.xpm -sc scount.xvg. Part of the >> output of dssp run is as follows. >> >> >> When prompted, what group did you choose for the analysis? >> >> -Justin >> >> >> @ s0 legend "Structure" >> >> >> @ s1 legend "Coil" >> >> >> @ s2 legend "B-Sheet" >> >> >> @ s3 legend "B-Bridge" >> >> >> @ s4 legend "Bend" >> >> >> @ s5 legend "Turn" >> >> >> @ s6 legend "A-Helix" >> >> >> @ s7 legend "5-Helix" >> >> >> @ s8 legend "3-Helix" >> >> >> 0 46 24 0 0 7 10 36 0 3 >> >> 10 39 26 0 0 15 4 35 0 0 >> >> 20 37 29 0 0 11 4 33 0 3 >> >> 30 37 32 0 0 11 2 35 0 0 >> >> 40 36 31 0 0 10 6 30 0 3 >> >> 50 41 30 0 0 9 10 31 0 0 >> >> Please suggest why I am not getting the actual number of residue >> in dssp file. >> When I follow the same procedure for full protein molecule >> simulation I get the same number of residue in dssp output as >> well as final.gro file >> shahid nayeem >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> 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 >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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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