[gmx-users] about how to create angle.index with specific angles

[lazaro monteserin]

Dear Dr. Lemkul it could be possible use that angle.index with the selected
dihedrals written by hand as index file for gmx angle for dihedral
Principal Component Analysis?                                     Kindly,
Lazaro

On Wed, Apr 29, 2020 at 7:23 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/29/20 5:01 PM, lazaro monteserin wrote:
> > Dear gromacs users,
> >
> > Is there any way to tell gmx mk_angndx to create the index file with
> > dihedral angles from a (.tpr) for specific atom numbers (atom level, e.g
> 1,
> > 2, 3) from my molecule?
>
> mk_angndx is designed for distributions of similar angles (e.g.
> evaluating force field sampling). If you want to compute specific
> angles, use make_ndx or simply write the index groups by hand.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Office: 301 Fralin Hall
> Lab: 303 Engel Hall
>
> Virginia Tech Department of Biochemistry
> 340 West Campus Dr.
> Blacksburg, VA 24061
>
> jalemkul at vt.edu | (540) 231-3129
> http://www.thelemkullab.com
>
> ==================================================
>
> --
> 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.
>