Please someone who has done dihedral pca can guide me to proceed further. Waiting for reply.
On Sat, Jan 3, 2015 at 1:35 PM, pratibha kapoor <kapoorpratib...@gmail.com> wrote: > Even I have referred the previous link for its definition. But then, how > should I select my backbone phi-psi dihedral angles to proceed further with > dihedral pca? > > Thanks > > On Sat, Jan 3, 2015 at 12:22 AM, pratibha kapoor < > kapoorpratib...@gmail.com> wrote: > >> Hi, >> >> Please correct me if I am wrong but I believe that since torsion angle >> omega is defined by 4 points in space namely Calpha (n) ,carbonyl carbon, >> nitrogen, and calpha (n+1), omiting or including carbonyl oxygen (i.e. >> using mainchain or backbone options) would not make a difference. >> Secondly, is it reasonable enough to exclude carbonyl oxygen atoms while >> calculating dihedral angles? >> I apologize beforehand for the ignorance. >> >> Waiting for reply. >> Thanks >> >> On Fri, Jan 2, 2015 at 7:36 PM, pratibha kapoor < >> kapoorpratib...@gmail.com> wrote: >> >>> Hi Bipin >>> >>> Thanks for the reply. >>> I have a small doubt won't selecting mainchain would also give owega >>> rather than only phi-psi angles? >>> >>> Thanks >>> >>> On Fri, Jan 2, 2015 at 6:14 PM, pratibha kapoor < >>> kapoorpratib...@gmail.com> wrote: >>> >>>> Hi, >>>> >>>> I would like to carry out dihedral pca with the dihedral angles (phi >>>> and psi) of the peptide backbone. My question is how should I select my >>>> dihedral angles? >>>> I am using >>>> mk_angndx -s *.tpr -n angle.ndx >>>> The angle.ndx file so created contains all the dihedral angles I guess. >>>> How should I select only the phi, psi dihedrals of peptide backbone? >>>> Also, I am not able to understand the meaning of >>>> [ Phi=180.0_2_33.50 ] >>>> etc. terms in the index file. >>>> Please guide me in proceeding further. >>>> >>>> Thanks >>>> >>> >>> >> > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
