[gmx-users] Dihedral pca

ruchi lohia ruchi.lohia15 at gmail.com
Mon Jan 19 17:39:58 CET 2015

Hi Pratibha

If you make the index file with only the backbone atoms the dangle.trr file
generated from

g_angle -f foo.xtc -s foo.tpr -n dangle.ndx -or dangle.trr -type dihedral

Gives you only the sine and cosine of backbone phi and psi dihedral angles
. You can check for it by converting your .trr  file to .gro using trjconv.

Hope it helps

Ruchi Lohia
PhD candidate
Rutgers university

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>

> 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
> 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
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