From owner-chemistry@ccl.net Mon Aug 14 10:20:00 2017
From: "Lizelle Lubbe lbbliz002##myuct.ac.za" <owner-chemistry#server.ccl.net>
To: CCL
Subject: CCL:G: How do you set up a hindered rotor calculation in Gaussian09?
Message-Id: <-52924-170814095322-31592-GerpU6gmzAlDMyLu3Y2xJw#server.ccl.net>
X-Original-From: "Lizelle  Lubbe" <lbbliz002\a/myuct.ac.za>
Date: Mon, 14 Aug 2017 09:53:18 -0400


Sent to CCL by: "Lizelle  Lubbe" [lbbliz002,myuct.ac.za]
Hi,

I am trained as a biochemist and still a novice at quantum mechanical 
calculations. The aim is to parameterize the metal site of a zinc 
metalloprotease for subsequent MD simulations in AMBER. Zinc is complexed to 
a glutamate, a water molecule and two histidines in a tetrahedral geometry. I 
have used Gaussian 09 to perform the geometry optimization and force constant 
calculation with the B3LYP/6-31G(d) basis set for all atoms except Zn for 
which the SDD pseudopotential was used. 

During the force constant calculation the following shows up in the log file:

> warning: explicit consideration of 37 degrees of freedom as vibrations may 
cause significant error

The user manual mentions use of freq=HinderedRotor to solve this.

Trying such a calculation, however, terminates with the following:

> Periodicity information is required for 4 bonds - please see 
readhinderedrotor in the user manual

The manual mentions that the rotational barrier cut-off height (kcal/mol), 
periodicity, symmetry number and multiplicity for rotatable bonds involving 
metals have to be specified through freq=readhinderedrotor. 

Unfortunately, I can't find any examples of metal bonds to amino acids where 
this was employed. Could someone please explain to me what these parameters 
mean? Also, where to find them/how to calculate them for Zn-N (histidine), Zn-
O (glutamate) and Zn-O (water) bonds and the format of these in the Gaussian 
input com file.

Kind regards

Lizelle 

lbbliz002(-)myuct.ac.za