[gmx-users] angke definition

Mark Abraham Mark.Abraham at anu.edu.au
Wed Oct 5 10:31:25 CEST 2011

On 5/10/2011 7:28 PM, Tsjerk Wassenaar wrote:
> 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.

Or g_traj -xvg none and a scripting language of choice.


> 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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