[gmx-users] angke definition

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Oct 5 10:28:30 CEST 2011

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.



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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

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

More information about the gromacs.org_gmx-users mailing list