From: Amanda Jenkins (amanda.jenkins1379_at_outlook.com)
Date: Sun Sep 25 2022 - 21:35:55 CDT

Hi Josh,

Thank you so much! This did work and now the dihedral angle calculations appear to be able to calculate values for phi and psi.

My follow-up question is, when I follow your instructions (after using dcd and psf as input files), within VMD, how do I delete multiple chain selections, save for the chain I want to keep to analyze? I need to do my analysis on chain C only but since the psf and dcd files present all three chains as chain P, as seen in the Sequence Viewer, all three chain angle results are lumped together in each calculated frame that Axel's script provides. This doesn't allow me to conveniently discriminate the results for chain C from the other chains.

As an aside, I just wanted to mention that after viewing the protein after following your instructions, I noticed that there appears to be one renegade water molecule and a couple of lone atoms (could be sodiums and chlorides) that respond to viewing GLY 311 in isolation, in addition to the actual GLY 311, and I don't understand why since sodium, chloride and water are not glycines. When I made a PDB of only the protein after following your instructions, the resulting PDB file had the same characteristic of treating chain C as two fragments and the renegade atoms were no longer present in that PDB file. I wasn't sure if these glycine "impostors" are crucial to creating a PDB that doesn't split chain C into fragments.

Thank you again Josh for your help, and if there's no convenient way to delete the other chains within VMD and run the dihedral angles script immediately afterards (that way I only get chain C dihedrals by keeping the glycine imposters), then I'll try processing the consolidated dihedrals file I mentioned above with scripting.

Amanda J.
________________________________
From: Vermaas, Josh <vermaasj_at_msu.edu>
Sent: Sunday, September 25, 2022 1:29 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,

Yeah, that does seem to be the root of the problem. When I loaded the pdb you sent along, VMD guesses the bonds present in the system based on a distance-based heuristic. As you noted, the long bond between the backbone nitrogen and the alpha carbon means that the distance based heuristic did not place a bond there. As a result, resid 311 is split between two “fragments”. A fragment in VMD is a connected set of atoms that get treated as one entity. Since there is no bond between the nitrogen and the carbon, the phi/psi calculations act as though Gly311 is not actually a residue within a protein, since the nitrogen is in a different fragment from the rest of the protein backbone. Since you *did* simulate this in NAMD, the solution is simple. Using the same selection you used to create your cut-down pdb file, *also* make a cut down psf, and load the psf (which has bond information) as well as the pdb file together when running your analysis. Alternatively, just analyze the psf/dcd together. Something like this is what I’d do:

mol new step3_charmm2namd.psf

mol addfile snapshot-1.dcd waitfor all

#Once you load these two in, there shouldn’t be a break at residue 311.

#Then you’d use your script as usual.

set mol [molinfo top]

set fp [open "BOB.txt" w]

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

set n [molinfo $mol get numframes]

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

$sel frame $i

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

-Josh

From: Amanda Jenkins <amanda.jenkins1379_at_outlook.com>
Date: Saturday, September 24, 2022 at 10:22 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,

I wanted to let you know that after zooming in on the problematic amino acid in isolation in VMD, it looks like that amino acid, for some strange reason, has an abnormal distance between its amino nitrogen and alpha carbon and VMD is not drawing a bond between these two atoms. I don't know if this might be the stumbling block for VMD to calculate the dihedral angles. Any thoughts on why this is happening? 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 isn’t 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