[AMBER] Periodicity of metal bond

From: Lizelle Lubbe <LBBLIZ002.myuct.ac.za>
Date: Tue, 15 Aug 2017 13:28:22 +0000

Dear Amber users,

I am using the MCPB.py program to parameterize Zn complexed to two histidines, a water molecule and a glutamate residue. After generating the small and large models in MCPB.py I use Gaussian 9 to optimize the geometry. In calculating the force constants the log file states:

warning: explicit consideration of 37 degrees of freedom as vibrations may cause significant error.
It was suggested online that specifying freq=HinderedRotor might solve this

After trying it the calculation terminates with the following:
Periodicity information is required for 4 bonds - please see readhinderedrotor in the user manual

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

The sp3-sp3 His(N) - Zn bond and water (O) - Zn bonds would be periodicity n=3 as far as I can tell.
Could someone please help me in understanding what the sp2-sp3 Glutamate (O) - Zn bond periodicity would be?
What would the format of this information be in the gaussian com file (input after geometry section)?

Kind regards

Lizelle Lubbe
PhD Chemical Biology candidate
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Received on Tue Aug 15 2017 - 06:30:03 PDT
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