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.
Mark
Cheers,
Tsjerk
On Wed, Oct 5, 2011 at 10:08 AM, Алексей Раевский<rayevsk...@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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