
23 Jan
2025
23 Jan
'25
9 p.m.
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