Justin, I produced the index file based on your suggestion, but when I ran the do_dssp, a completely different result was spit out comparing to what the whole protein analysis had given. Any ideas on why that might have happened?
Paymon On Wed, 2010-10-06 at 14:42 -0400, Justin A. Lemkul wrote: > > Paymon Pirzadeh wrote: > > Hello, I want to check the secondary structure of protein at particular > > residues. Since dssp needs all main chain atoms, does the following command > > at the make_ndx prompt makes the correct index file? > > You can answer that yourself by looking at the resulting index file. > > > 5 | r 1 | r 10-11 |r 14-17 | r 20-21 | r 26-32 | r 42 | r 45 > > > > To get these groups to merge, I think you probably need to do 5 & r 1 | ... > > -Justin > > > (Main chain atom of particular residues). regards, > > > > Paymon > > > > -- > ======================================== > > 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/Support/Mailing_Lists/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/Support/Mailing_Lists
