Oops, I got it wrong, ChimeraX can write PQR format! To do that, you have to use the "save" command with the option "pqr true": <https://rbvi.ucsf.edu/chimerax/docs/user/commands/save.html#pdb> More about PQR: <https://rbvi.ucsf.edu/chimerax/docs/user/formats/pdbintro.html#PQR> Sorry about that, Elaine
On Dec 6, 2023, at 11:57 AM, Elaine Meng via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Dan, As Eric said, those last columns are the formal charge (integer only), whereas Dock Prep adds partial (non-integer) charges to atoms. ChimeraX does not output the formal charge, which is an optional part of PDB format, whereas we do make every effort to adhere to PDB standards when writing the file. However, if you want partial charges included in a file, you have to use a different format, namely Mol2.
Maybe the docking program you mention uses PDBQT or PQR format, neither of which are the same as standard PDB format. Autodock and Autodock Vina use PDBQT format, if I remember correctly. PDBQT format has columns for partial charge (Q) and atom type (T), and PQR has columns for partial charge (Q) and radius (R) even though the first part of each line looks the same as PDB format. However, ChimeraX does not write either of those formats.
Best, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Dec 6, 2023, at 10:04 AM, Daniel Hsu via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
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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