Re: [AMBER] parameters for benzene, pyerene, anthracene, and coronene

From: David A Case <david.case.rutgers.edu>
Date: Mon, 14 Dec 2020 09:05:40 -0500

On Sun, Dec 13, 2020, Bouthe´na KERKENI wrote:

>I want to compute Infrared Res spectra of parameters for benzene,
>pyerene, anthracene, and coronene.

>I used gaussian to employ the amber parameters for atom types CA and HA.

I doubt that people here know much about how Gaussian interacts in Amber
parameters. Further, it's not clear exactly what you did to "employ
amber parameters for atom types CA and HA". It's likely better to ask
you question at Gaussian forums.

>My question is with respect to these parameters how they are obtained
>and do they include for anharmonic effects, any reference will be very
>helpful ?

Amber force field do not include any anharmonic terms.

>Also, how come a central carbon will have the same type as a peripheral
>carbon? when going from benzene to coronene for example through pyerene,
>anthracene and naphthalene?

I don't know how you got to this situation. For force fields, Amber
users would generally use GAFF2 atom types, not protein atom types.
Note that proteins don't have entities like anthracene, etc., so one
should not expect Amber protein parameters to be appropriate for such
compounds.

....dac


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Received on Mon Dec 14 2020 - 06:30:08 PST
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