From: Josh Vermaas (
Date: Fri Sep 23 2022 - 07:54:53 CDT

Hi Amanda,

How are you calculating phi/psi angles? I'm betting that your script
isn't updating the selection over your trajectory. A way to confirm this
visually is to label the specific dihedral of interest (on the VMD main
window Mouse->Label->Dihedral), and animate through your trajectory. I
suspect you'll see non-zero values. It is basically impossible for a
trajectory to give you exactly a 0.0 dihedral for all frames, but it is
relatively easy (and I've done it) to forget to update your selection
within Tcl so that VMD is calculating on the right set of coordinates.


On 9/23/22 6:14 AM, Amanda Jenkins wrote:
> Dear community,
> I have results/PDB trajectories from several MD simulations/repeats of
> a protein composed of several chains.  For one of the chains, one of
> the amino acids, always has values of 0.0 for both phi and psi angles
> throughout the trajectory simulation.  This is observed throughout
> each different set/repeat of simulation results and at the same amino
> acid in the same chain.  I have RMSD aligned each individual
> trajectory/simulation result set, so my initial theory was that maybe
> this amino acid in question is serving as the "anchor" point upon
> which all the other snapshots are superimposed for a given simulation
> set, but it still seems a bit odd to me that both phi and psi angles
> would be perfectly 0.0 at every single trajectory snapshot.  I have
> other amino acids that have small/fractional phi and psi angles so I
> am suspicious that this perfect set of 0.0 phi and psi angles might be
> an artifact of some sort and not an actual physical phenomenon.
> Would someone please tell me what could be causing this situation?  Is
> it an artifact?
> For additional information, my total simulation time is 200
> nanoseconds with a snapshot being printed every 1 nanosecond, and this
> is done for all of my distinct simulation result sets/repeats.
> Thanks for any insight anyone can provide.
> Amanda J.

Josh Vermaas
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University