From owner-chemistry@ccl.net Tue Sep 26 19:18:00 2017 From: "Zachary B Smithline zachary.smithline^yale.edu" To: CCL Subject: CCL:G: Gaussian ONIOM Link Atoms Message-Id: <-53015-170926191613-2513-jShlJeYtnjKXGtLCg6zBpQ _ server.ccl.net> X-Original-From: "Zachary B Smithline" Date: Tue, 26 Sep 2017 19:16:11 -0400 Sent to CCL by: "Zachary B Smithline" [zachary.smithline|yale.edu] 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 (http://gaussian.com/oniom_technote/), the second example under 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 5." Thank you in advance! -- Zachary Smithline Lab of Thomas Steitz Departments of MB&B and Chemistry Yale University email: zachary.smithline^-^yale.edu