Hi Dr. Simmerling.
First of all, yes, I'm sorry, I was meaning the ff19sb force field.
And thanks for the clarification: the QM calculation level for the dihedral torsions indeed changed *a lot* through time. ff19sb is proof of that, and its paper kind of its testimony. ;)
One additional question that concerns the "traditional" (lowest and highest energy conformations in a torsion rotation) torsions paranetrizatioms that is present at least in ff94/96, but I think still works at least in gaff: while in free rotating bonds it is simple to find and study those (two) conformations, on the opposite case it is sometimes hard to even picture it. I mean, how are/were the maximum energy dihedral torsions calculated for ethene, or even worst for a X-CA-CA-X dihedral? With 90º distorted ethene and benzene molecules?
Thanks a lot for all help,
Best regards,
Jones
Em 14 de fevereiro de 2024 09:00:52 BRT, Carlos Simmerling <carlos.simmerling.gmail.com> escreveu:
>There are a variety of force fields and also training strategies. I am not
>sure what you mean by "AMBER19". Amber itself is the software, and the
>force fields have different names. If you mean the protein ff19sb force
>field, I suggest reading the original article for details on the QM level
>for training dihedrals (which included aqueous solvation). Others, such as
>GAFF for small molecules, differ.
>
>On Tue, Feb 13, 2024, 10:02 PM Jones De Andrade via AMBER <amber.ambermd.org>
>wrote:
>
>> Hi all.
>>
>> I' looking for an answer that will probably quite straightforward here.
>> ;)
>>
>> I'm performing the parametrization of some dihedral torsions. I know
>> from older amber versions and its papers (i.e, Cornell JACS 1995 and Fox
>> JPCB 1998) that it used to be done at MP2/6-31G*//HF/6-31G* level.
>>
>> However, since Amber94/96 a lot of evolution happened until AMBER19, so
>> I want to ask if there was any changes (possible improvements) on the
>> "protocol" concerning *especifically* dihedrals torsions
>> parametrization, or it it is still maintained at the same level.
>>
>> Thanks a lot in advance,
>>
>> Best regards,
>>
>> Jones
>> --
>> Jones de Andrade
>> (jdandrade.iq.ufrgs.br)
>> DFQ/IQ/UFRGS
>> Lattes: http://lattes.cnpq.br/6675936210583999
>> Orcid: https://orcid.org/0000-0003-3429-8119
>> ResearcherID: https://publons.com/researcher/AAC-5337-2019/
>>
>> _______________________________________________
>> 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 Thu Feb 15 2024 - 05:30:02 PST
