[gmx-users] question regarding gmx helix orientation

[SHAHEE ISLAM]

hello,
by using gmx gangle, i am trying to calculate the angle between protein and
bilayer,
gmx gangle -f *.xtc -s *.tpr -n *.ndx -g1 vector -g2 plane -group1 -group2.
but the error i am getting is
Number of positions in selection 1 in the first group not divisible by 2
my questions are
1. how can i select the index file so that angle will be calculated between
protein and bilayer.
2. should i mention group name in the gmx gangle calculation command.
the total atoms of protein is 283
and for bilayer it is 9360.

thanking you
shahee

On Sat, Dec 14, 2019 at 6:23 AM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 12/13/19 7:06 AM, SHAHEE ISLAM wrote:
> > Yes ,I am using cg model.
>
> Use gmx gangle.
>
> -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.
>