Chemical Forums
Chemistry Forums for Students => Physical Chemistry Forum => Topic started by: Lizelle on August 14, 2017, 09:59:56 AM
-
Hi,
I am trained as a biochemist and still a novice at quantum mechanical calculations. My 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