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<https://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#...>, 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<mailto: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! **CONFIDENTIALITY NOTICE** This e-mail communication and any attachments are for the sole use of the intended recipient and may contain information that is confidential and privileged under state and federal privacy laws. If you received this e-mail in error, be aware that any unauthorized use, disclosure, copying, or distribution is strictly prohibited. If you received this e-mail in error, please contact the sender immediately and destroy/delete all copies of this message. _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu<mailto:chimerax-users-leave@cgl.ucsf.edu> Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/