[AMBER] angles analysis

From: Fabian Glaser <fabian.glaser.gmail.com>
Date: Sun, 22 Sep 2019 15:15:44 +0300

Dear Amber experts,

I would like your opinion on the following:

I am interested to compute a certain angle involving a fixed atom and two other atoms which change during the trajectory depending on their distance to the fixed atom. That means that at any given frame, one atom is always the same and the other two atoms forming the angle need to be identified interactively.

I wonder what is the simplest way to do it.

I know I can write a python script using biopython from scratch but is there an effective way of using cpptraj to identify the atoms on the fly in each frame and measure their angle? Alternatively is there a good tool to analyze the trajectory which could be use to do it?

Any ideas will be appreciated.



Fabian Glaser PhD

Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa, Israel
Web http://bku.technion.ac.il/
Tel +972 (0) 4 8293701

AMBER mailing list
Received on Sun Sep 22 2019 - 05:30:03 PDT
Custom Search