[gmx-users] Dihedral pca

[Tsjerk Wassenaar]

I think it is... see http://en.wikipedia.org/wiki/Dihedral_angle

Cheers,

Tsjerk

On Fri, Jan 2, 2015 at 10:00 PM, bipin singh <bipinelmat at gmail.com> wrote:

> 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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-- 
Tsjerk A. Wassenaar, Ph.D.