Hi Jade, Well, the answer is a little more complicated, because getting the wrong net charge for some nonstandard residue like a ligand is probably because ChimeraX got the atom type wrong for one or more atoms. For these residues, instead of running "dockprep," which includes adding hydrogens and charges, you could: (1) run "addh" <https://rbvi.ucsf.edu/chimerax/docs/user/commands/addh.html> (2) run "addcharge nonstd" and specify the net charge which would get passed to antechamber with -nc <https://rbvi.ucsf.edu/chimerax/docs/user/commands/addcharge.html> HOWEVER, that would probably still give an incorrectly protonated molecule if the atom types are wrong in the first place, even if you force the net charge to be the correct amount. To really try to make it correct, you could open the structure, label the ligand with its atom types, and change the atom types that are wrong before using "dockprep". See for example this previous post for how to label with atom types and change the atom types <https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/...> List of atom types and their descriptions: <https://www.rbvi.ucsf.edu/chimerax/docs/user/atomtypes.html> If you can't figure out what is going on with the ligand, however, when this problem happens you could instead use menu: Help... Report a Bug and either attach the session or say what PDB ID and residue are having this problem, and what net charge you expect it to have, so that we could try to diagnose the problem and suggest a solution. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco

On Jan 23, 2025, at 9:00 PM, Jade Shi via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, I am trying to use dockprep to prepare PDB files with ligand molecules for subsequent modeling and analysis. I am currently using the "dockprep" command with no additional arguments. However, I find that occasionally when calculating partial charges using antechamber/AM1-BCC, ChimeraX assigns an incorrect total charge to the ligand resulting in an incorrect charge distribution. Is there a way to specify this manually, i.e. the equivalent of supplying the -nc flag when using antechamber directly?

Thanks a lot! Jade _______________________________________________ ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/