CCL:G: Gaussian ONIOM Link Atoms

 Sent to CCL by: "Zachary B Smithline" [zachary.smithline|]
 Dear All,
 I have a simple question regarding ONIOM link atoms for QM/MM Gaussian jobs that
 use Amber
 for the MM layer. In this link (, the second example
 the heading "Input Examples" presents a sample Gaussian ONIOM input
 deck with Amber for the
 low layer. Here, there is notation indicating the link atom (LA) used to cap
 given atoms in the QM
 region for the QM region-only part of the ONIOM calculation -- for example
 "H-HA-0.1  3." My
 question is where do the LA atom types and charges come from? And do they even
 matter? If
 they do matter, the examples in the sample input deck in the link above don't
 even seem to be
 consistent. Consider, for example, "H-HC-0.1  5." This indicates that
 a LA of Amber type HC, an
 aliphatic carbon, is connected to atom 5. Atom 5, however, is a CA carbon, so it
 is aromatic. This
 implies that "H-HC-0.1  5" should actually read "H-HA-0.1
 Thank you in advance!
 Zachary Smithline
 Lab of Thomas Steitz
 Departments of MB&B and Chemistry
 Yale University
 email: zachary.smithline^-^