if you haven't looked at the Amber tutorials page already there are some
there that might be helpful such as
http://ambermd.org/tutorials/basic/tutorial4b/index.php
On Mon, Dec 14, 2020 at 9:35 AM Boutheïna KERKENI <
boutheina.kerkeni.obspm.fr> wrote:
> Thanks for the replies. Where are the Gaff2 parameters please, so I can
> retrieve them for my specific calculations?
>
> Regards
> Boutheïna
>
>
>
> > On Dec 14, 2020, at 3:15 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
> >
> > 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.
> > https://pubs.acs.org/doi/full/10.1021/ja026825l
> >
> > On Mon, Dec 14, 2020 at 9:05 AM David A Case <david.case.rutgers.edu>
> 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
> >>
> >>
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Dec 14 2020 - 07:00:07 PST
