[gmx-users] Dihedral pca

[bipin singh]

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>
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
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>