For extracting all the atoms involved in the phi-psi dihedral, you can use make_ndx and select Mainchain group, then you can extract all the dihedrals from the trajectory using the below command:
g_angle -f foo.xtc -s foo.tpr -n dangle.ndx -or dangle.trr -type dihedral As described here: http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA ------------------------------ Thanks and Regards, Bipin Singh 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. > -- 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.