On Jun 14, 2010, at 10:48 AM, Francesco Pietra wrote:
With the combined pdb file, does dockprep operate on single molecules
one after the other, so that it will not encounter obstacles even for
many (more complex) ligands?
I think this will be okay. Chimera ignores sibling submodels (e.g. #0.2 is a "sibling" of #0.1) when adding hydrogens so you will be okay if all your ligands come from one file.