[gmx-users] re:surface normal direction

Berk Hess gmx3 at hotmail.com
Thu Mar 4 14:39:00 CET 2004

>>Dear All,
> >>Is ther a tool in the gromacs package to define the
> >>surface normal direction of a membrane protein based
> >>on orientation of alpha helices.
> >how about g_bundle?
>Since this may be of general interest could you
>describe how to get the vector pointing to +z direction
>with g_bundle and perhaps after that rotate protein
>so that z axis points to 001 direction.
>I managed to get nice rasmol picture of the membrane protein with
>axis on it, but could not work out the explicit z direction from the
>output files of g_bundle.

I did not write g_bundle with this in mind, you can not get the surface
normal direction out of it. If you think that the average helix direction
is a good indication for the surface normal, you can get the direction
by calculating the center of mass with g_traj of the total top group and
the total bottom group you used as input for g_bundle.


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