I am trying to setup QM/MM calculations with QChem using user-defined connectivity and MM parameters. But the official manual is not detailed about some options. Mostly I am interested in the procedure of accounting angles and torsions across QM/MM linkage. How it is usually calculated during QM/MM? And is there any additional keys in $rem section to control QM/MM job for QChem? Thanks!
The Q-Chem manual edition 5.2 is much better at describing QM/MM
However, to answer your main question there are no angles and torsions across a link atom. The link atom is a fictitious hydrogen that is added when you break the QM and MM region at a bond. This is done to maintain the proper valency/avoid dangling bonds in the QM region. The MM region is also affected in some methods, for example in additive QM/MM schemes the fractional charge that occurs due to partitioning the system into QM and MM regions is smeared out amongst the remaining MM atoms.
Q-Chem automatically insert the link atoms depending on the definitions of the QM and MM regions.
Link atoms for the ONIOM model and YinYang atoms for the Janus model are not specified in the $qm_atoms section, as these are inserted automatically whenever a bond connects a QM atom and an MM atom.
Note however, that this only works if the linked atom is a carbon.