[gmx-users] angke definition

[Tsjerk Wassenaar]

Hey :)

Would g_sgangle be capable of what you want?

Otherwise, your best bet seems to be writing the atoms involved to an
easily readable format (.gro/.pdb) and do the math in Python. I can
send you a backbone Python script for reading .gro/.pdb trajectories
if you want.

Cheers,

Tsjerk

On Wed, Oct 5, 2011 at 10:08 AM, Алексей Раевский <rayevsky85 at gmail.com> wrote:
> Hi, i need your help again! this time in the selection of analyzing tools
> and methods... I've found a water molecule near one of the ligand atoms.
> It's stabile enough and the distance is about 3.3 A. But I want to make some
> measurments, exactly angle degree identification. I want to calculate the
> frequence of forming of angle (about 90 degree) between oxygen of the water
> and the plane (formed by the atom of the ligand and several atoms around (it
> is a first CA atom and carboxyl group CA-C-O-OH of aminoacid)). But a
> perpendicular from OW is connected exactly to C atom of carboxyl group. In
> other case gromacs is trying to calculate an angle between OW and the whole,
> unlimited plane... Can I do such analyze? Ormay be you can give me  some
> advices
> Thank you!
> --
>
>
> Nemo me impune lacessit
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands