[gmx-users] Dihedral pca

[pratibha kapoor]

Please someone who has done dihedral pca can guide me to proceed further.
Waiting for reply.

On Sat, Jan 3, 2015 at 1:35 PM, pratibha kapoor <kapoorpratibha7 at gmail.com>
wrote:

> 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?
>
> Thanks
>
> 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
>>>>
>>>
>>>
>>
>