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

From: Carlos Simmerling <>
Date: Mon, 14 Dec 2020 09:15:19 -0500

we published a study a while ago using pyrene with DNA, and parameters were
included in the SI. These did use CA, but you should note that this was a
long time ago (2002). I would not do it this way now, I would use GAFF2 as
Dave Case suggested.

On Mon, Dec 14, 2020 at 9:05 AM David A Case <> wrote:

> On Sun, Dec 13, 2020, Boutheïna 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 - 06:30:09 PST
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