VMD-L Mailing List

From: Navid Shervani-Tabar (nshervt_at_gmail.com)
Date: Wed Sep 16 2020 - 14:01:30 CDT

Dear VMD experts,

I have a trajectory of alanine dipeptide molecule (from
https://markovmodel.github.io/mdshare/ALA2/#alanine-dipeptide) and would
like to save the conformation label (alpha_L, alpha_R, beta, etc) at each
timestep. I was wondering if VMD can do this. I have two files available:
1) .pdb file and 2) .xtc file. I'm able to load the data and save the
trajectory coordinates as an xyz file and plot the Ramachandran plot, but I
can't find how to assign conformation type based on phi and psi dihedral
angles. Thanks!

Best,
Navid