[gmx-users] Dihedral pca

bipin singh bipinelmat at gmail.com
Fri Jan 2 14:22:23 CET 2015

For extracting all the atoms involved in the phi-psi dihedral, you can use
make_ndx and select Mainchain group, then you can extract all the dihedrals
from the trajectory using the below command:

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

As described here: http://www.gromacs.org/Documentation/How-tos/Dihedral_PCA

Thanks and Regards,
Bipin Singh

On Fri, Jan 2, 2015 at 6:14 PM, pratibha kapoor <kapoorpratibha7 at gmail.com>

> 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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