Hi Dr. Simmerling. Thanks for the prompt answer (and sorry for any mistyping: using the phone since we got our optical link severed here at university).
Yes, that is what I called "traditional" protocol. My point is that this is the reported protocol for the original amber ff94/96 (only difference is that instead of fitting it would mostly focus on just the overall rotation energy barrier), and I even think it is the parametrization technique used for gaff, but it still managed no stablish the parameters of a X-CA-CA-X dihedral torsion (basically, a benzene ring).
It always bothered me how it could actually be done on that way for such aromatic atoms for the same concern you expressed: the energy would skyrocket.
So, how was the original X-CA-CA-X dihedral torsion force constant parametrized for ff94/96? Does anybody has any idea?
Thanks a lot again, and best regards,
Jones
Em 15 de fevereiro de 2024 13:39:42 BRT, Carlos Simmerling <carlos.simmerling.stonybrook.edu> escreveu:
>Hi Jones,
>not sure I'm following you. In many fitting protocols, one rotates around
>the bond of interest and calculates energy using QM or other reference
>method, and then does the same in MM, then fits parameters to minimize the
>difference. Are you asking how this is done for something like a double
>bond? the energy would be much higher, and for benzene likely impractical
>due to the coupling with bonds in the ring. but ethene can be done, and the
>barrier calculate from the 90 deg geometry.
>is that what you were asking?
>
>
>On Thu, Feb 15, 2024 at 7:58 AM Jones de Andrade via AMBER <
>amber.ambermd.org> wrote:
>
>> 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/
>> >>
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Received on Thu Feb 15 2024 - 09:30:02 PST
