From: Amanda Jenkins (amanda.jenkins1379_at_outlook.com)
Date: Sat Sep 24 2022 - 17:20:27 CDT

Hi Josh,

I sent you the pdb and psf files. Please let me know if you were able to download and open them. Thanks.

Amanda J.
________________________________
From: Vermaas, Josh <vermaasj_at_msu.edu>
Sent: Saturday, September 24, 2022 12:28 PM
To: Amanda Jenkins <amanda.jenkins1379_at_outlook.com>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Ramachandran Dihedral Angles Suspiciously Constant

Huh. Could you send the psf/pdb off list? That is actually what dictates what VMD recognizes as protein, and would be more helpful in figuring out why your protein isnít being picked up as protein.

-Josh

From: Amanda Jenkins <amanda.jenkins1379_at_outlook.com>
Date: Friday, September 23, 2022 at 10:19 PM
To: "Vermaas, Josh" <vermaasj_at_msu.edu>, "vmd-l_at_ks.uiuc.edu" <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Ramachandran Dihedral Angles Suspiciously Constant

Hi Josh,

Yes, this script was indeed originally authored by Axel Kohlmeyer.

The problematic amino acid in question is not a terminal amino acid but it is actually located in the middle of the protein which is what surprised me with the 0.0 at all snapshots. I do not have any other molecules or ligands in the system, just my protein alone.

I have attached to this e-mail a representative conf file with the settings I used. Hopefully it can help diagnose the issue. Thanks for your help.

Amanda J

________________________________

From: Josh Vermaas <vermaasj_at_msu.edu>
Sent: Friday, September 23, 2022 3:36 PM
To: Amanda Jenkins <amanda.jenkins1379_at_outlook.com>; vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Ramachandran Dihedral Angles Suspiciously Constant

Hi Amanda,

This is a fun one! You did indeed do exactly what I would have done, and use the "$sel frame $i" to set the correct frame. The update is strictly speaking not needed, unless the selection changes as a function of time. This looks like what Axel suggested back in 2005 (https://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/4885.html$>), so this looks reasonable.

But I think I now understand the problem. Is the amino acid that is reporting consistently 0 either at the beginning or end of the chain? The first amino acid doesn't have a phi angle, and the last amino acid doesn't have a psi angle. Likewise, if you had something that wasn't a protein in your system, but *did* have a CA atom, that might also not have a phi or psi angle. In VMD, not having a phi or psi angle manifests as *always* reporting 0. What I did to test this was to take your script and run it against the ubiquitin in a box simulation from the NAMD tutorial. That made it clear that your script was actually fine, and that you might be running into something weird with how your system is constructed.

-Josh

On 9/23/22 2:30 PM, Amanda Jenkins wrote:

Hello Josh,

I am calculating the dihedral angles (phi and psi) using a Tcl TkCon script which is below:

set mol [molinfo top]

set fp [open "BOB.txt" w]

set sel [atomselect $mol "all and name CA"]

set n [molinfo $mol get numframes]

for {set i 0} {$i < $n} {incr i} {

$sel frame $i

$sel update

puts $fp "\# frame: $i"

set a [$sel num]

for {set j 0} {$j < $a} {incr j} {

puts $fp "[expr $j + 1] [lindex [$sel get {resname phi psi}] $j]"

}

}

$sel delete

close $fp

Is the line $sel update (bolded) insufficient to update the trajectory? Thanks.

Amanda J.

________________________________

From: Josh Vermaas <vermaasj_at_msu.edu><mailto:vermaasj_at_msu.edu>
Sent: Friday, September 23, 2022 7:54 AM
To: Amanda Jenkins <amanda.jenkins1379_at_outlook.com><mailto:amanda.jenkins1379_at_outlook.com>; vmd-l_at_ks.uiuc.edu<mailto:vmd-l_at_ks.uiuc.edu> <vmd-l_at_ks.uiuc.edu><mailto:vmd-l_at_ks.uiuc.edu>
Subject: Re: vmd-l: Ramachandran Dihedral Angles Suspiciously Constant

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.

-Josh

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
vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io
--
Josh Vermaas
vermaasj_at_msu.edu<mailto:vermaasj_at_msu.edu>
Assistant Professor, Plant Research Laboratory and Biochemistry and Molecular Biology
Michigan State University
vermaaslab.github.io