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
Received on Mon Dec 14 2020 - 07:00:06 PST
