From: Daniel Guion (danielguion_at_g.ucla.edu)
Date: Fri Dec 13 2024 - 16:19:19 CST

Hello,

I am trying to run mutator on a solvated system with residues that have
alternative protonation (ASPP, GLUP, and LSN; from propka), which already
have patches in "/Applications/VMD
1.9.4a57-arm64-Rev12.app/Contents/vmd/plugins/noarch/tcl/readcharmmtop1.2/top_all36_prot.rtf".
It makes sense to me that I don't have to create custom new patches in this
file to specify them in the psf since they are relatively common
alternative protonation states of standard protein residues.

Here is how I specified an example patch at the top of my psf file (reduced
to 1 patch for troubleshooting)
" 2 !NTITLE
 REMARKS patch ASPP A3:137"

When I run mutator, though, it crashes and I get this error

" Mutator: Writing temporary files for non-protein components

psfgen) Info: writing psf file mtemp-nprot.psf

psfgen) total of 1054889 atoms

psfgen) total of 1052154 bonds

psfgen) total of 664357 angles

psfgen) total of 526655 dihedrals

psfgen) total of 3176 impropers

psfgen) total of 0 explicit exclusions

psfgen) Structure requires EXTended PSF format

psfgen) total of 0 cross-terms

psfgen) no residue 137 of segment A3

/Applications/VMD 1.9.4a57-arm64-Rev12.app/Contents/MacOS/startup.command:
line 7: 83723 Trace/BPT trap: 5
"$p/../Resources/VMD.app/Contents/MacOS/VMD"
$*

Saving session...

..copying shared history...

..saving history...truncating history files...

..completed.

[Process completed]"

If I remove the patch line from my psf file, VMD does not crash and instead
runs to completion - however the script notes a warning that the
coordinates for the extra hydrogen atom for that residue cannot be guessed.
"psfgen) reading coordinates from pdb file mtemp-A3.pdb for segment A3

psfgen) Warning: failed to set coordinate for atom HD2 ASP:137 A3
..

Mutator: System net charge after mutation: -40.7995137386024e

Mutator 1.3 completed successfully.

WARNING: mutations were performed using psfgen. Original backbone

atom coordinates were used for positions of backbone atoms of the

new amino acid(s). Original coordinates of sidechain atoms named

identically to atoms of the new amino acid(s) were used for positions

of the new sidechain atoms. The positions of the remaining atoms

were guessed using internal coordinates for each amino acid. It is

therefore *highly recommended* to visually inspect the resulting

structure and perform a minimization/equilibration of the system."

When I look at the output psf and pdb file without adding the patch to the
psf, it looks okay except I don't have the proton like in the input anymore
- it removed it. Plus the charge of the system is off because I don't have
the protonation I solvated (water+ions) with (-40.7995137386024e); recall I
am just showing 1 alternative protonation state in this message for
troubleshooting, but my whole system contains other alternative
protonations (from propka).

I then tried purposefully changing the patch line to have the wrong
formatting by removing the ":"

" REMARKS patch ASPP A3 137"
instead of
" REMARKS patch ASPP A3:137"

And the mutator no longer recognizes that I have a patch specified in the
psf, which was a nice validation that I have the correct patch notation, I
suppose.

I’ve also ensured that the residue numbers and segment IDs match between
the PSF and PDB files

PSF -
    6958 A3 137 ASP N NH1 -0.470000 14.0070 0
    6959 A3 137 ASP HN H 0.310000 1.00800 0
    6960 A3 137 ASP CA CT1 0.070000 12.0110 0
    6961 A3 137 ASP HA HB1 0.090000 1.00800 0
    6962 A3 137 ASP CB CT2 -0.210000 12.0110 0
    6963 A3 137 ASP HB1 HA2 0.090000 1.00800 0
    6964 A3 137 ASP HB2 HA2 0.090000 1.00800 0
    6965 A3 137 ASP CG CD 0.750000 12.0110 0
    6966 A3 137 ASP OD1 OB -0.550000 15.9994 0
    6967 A3 137 ASP OD2 OH1 -0.610000 15.9994 0
    6968 A3 137 ASP HD2 H 0.440000 1.00800 0
    6969 A3 137 ASP C C 0.510000 12.0110 0
    6970 A3 137 ASP O O -0.510000 15.9994 0

PDB -
ATOM 6958 N ASP X 137 83.530 3.953 -57.743 1.00 0.00 A3
ATOM 6959 HN ASP X 137 84.010 4.446 -58.465 1.00 0.00 A3
ATOM 6960 CA ASP X 137 84.142 3.929 -56.431 1.00 0.00 A3
ATOM 6961 HA ASP X 137 84.144 2.906 -56.087 1.00 0.00 A3
ATOM 6962 CB ASP X 137 85.559 4.470 -56.466 1.00 0.00 A3
ATOM 6963 HB1 ASP X 137 85.928 4.585 -55.425 1.00 0.00 A3
ATOM 6964 HB2 ASP X 137 85.554 5.463 -56.964 1.00 0.00 A3
ATOM 6965 CG ASP X 137 86.499 3.570 -57.209 1.00 0.00 A3
ATOM 6966 OD1 ASP X 137 87.627 4.012 -57.493 1.00 0.00 A3
ATOM 6967 OD2 ASP X 137 86.117 2.416 -57.490 1.00 0.00 A3
ATOM 6968 HD2 ASP X 137 86.757 1.882 -57.966 1.00 0.00 A3
ATOM 6969 C ASP X 137 83.285 4.762 -55.513 1.00 0.00 A3
ATOM 6970 O ASP X 137 83.301 4.588 -54.306 1.00 0.00 A3

What is the issue that is happening here? I appreciate the help.

-- 
Daniel Guion (he/him)
Graduate Student in Biochemistry, Molecular and Structural Biology
Department of Chemistry and Biochemistry
University of California, Los Angeles
danielguion_at_g.ucla.edu