Hi Eric

Thank you for this explanation!

While not an expert at reading PDB records, I noticed that Protein Prep output in PDB from one program contains annotations that pertain to unit charge. This does not appear to be incorrect because another platform running docking (and other processes) reads it fine. e.g., lines below:

ATOM      1  N   PRO A 113       6.373   5.875   9.398  1.00 31.24           N1+

.

ATOM    256  NH2 ARG A 129      -9.487 -21.448  13.950  1.00 28.43           N1+

.

ATOM    567  OD2 ASP A 148     -11.479   2.884   0.139  1.00 15.41           O1-

But what’s bothersome, and unfortunate for me, the platform I use rejects ChimeraX PDB output processed with Dock Prep, error message uninsightful, but it may be possible to ask support to what the error pertains. And, it does not support mol2 structure input.

Any suggestion/comments are much appreciated.

Thanks

Dan

From: Eric Pettersen <pett@cgl.ucsf.edu>
Sent: Wednesday, December 6, 2023 9:21 AM
To: Daniel Hsu <dkhsu@ucdavis.edu>
Cc: chimerax-users@cgl.ucsf.edu
Subject: Re: [chimerax-users] Add charge to PDB fails

Hi Daniel,

ChimeraX computes partial charges for atoms.  As per the PDB format for ATOM records, the "charge" columns are for formal charges -- there are only two columns for charge information which therefore couldn't possibly contain partial charges.  Some other formats that ChimeraX can save (such as Sybyl Mol2) can retain partial charge information.

--Eric

Eric Pettersen

UCSF Computer Graphics Lab

On Dec 5, 2023, at 7:35 PM, Daniel Hsu via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi All

What might cause this action to fail, pH=7.4, H added to protein before adding charge? No errors were thrown.

Both DOCK-Prep, and adding H then charge both do not change the PDB file (no charges added to respective atoms). Log reports “Using Amber 20 recommended default charges and atom types for standard residues”

Alternative command ‘addcharge standardizeResidues 5BU,CSL,MSE,UMS’ reports “Using Amber 20 recommended default charges and atom types for standard residues” and no errors but don’t add charges to saved PDB file.

Charges are added with another structure editor.

Thanks for insights!

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