[gmx-users] Dihedral pca

[bipin singh]

I don't think the definition of omega dihedral which you have written is
correct,


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

On Sat, Jan 3, 2015 at 12:22 AM, pratibha kapoor <kapoorpratibha7 at 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 <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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