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 <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 > > -- > gmx-users mailing list gmx-users@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-requ...@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 -- gmx-users mailing list gmx-users@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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists