[gmx-users] Dihedral pca

[pratibha kapoor]

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
>>
>
>