[gmx-users] Dihedral pca

[bipin singh]

Yes, may be it will include omega too, but I am not sure. In that case, you
may select only the backbone atoms.


------------------------------
Thanks and Regards,
Bipin Singh

On Fri, Jan 2, 2015 at 7:36 PM, pratibha kapoor <kapoorpratibha7 at 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 <kapoorpratibha7 at 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
> >
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