Re: [AMBER] Periodicity of metal bond

From: Pengfei Li <>
Date: Tue, 15 Aug 2017 09:50:00 -0500

Hi Lizelle,

I did not met this kind of issue before. Maybe you can try to optimize the structure using lower level of theory first and then re-optimized it using the level of theory you are using now.

Kind regards,

> On Aug 15, 2017, at 8:28 AM, Lizelle Lubbe <> wrote:
> Dear Amber users,
> I am using the program to parameterize Zn complexed to two histidines, a water molecule and a glutamate residue. After generating the small and large models in 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 - 08:00:03 PDT
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