[gmx-users] Dihedral pca

pratibha kapoor kapoorpratibha7 at gmail.com
Sat Jan 3 09:05:39 CET 2015

Even I have referred the previous link for its definition. But then, how
should I select my backbone phi-psi dihedral angles to proceed further with
dihedral pca?


On Sat, Jan 3, 2015 at 12:22 AM, pratibha kapoor <kapoorpratibha7 at gmail.com>

> 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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