Atom types are not always just about local chemical environment, often
additional types are defined in order to allow independent parameters in
cases where partial charges differ, or combined fitting led to worse fit to
training data.
On Sat, May 25, 2024, 8:01 AM Jones De Andrade via AMBER <amber.ambermd.org>
wrote:
> Hi all.
>
> I was studying the atom types list of the ambe19sb force field (paper
> supporting information), mostly with help from amber94 aminoacid and
> atoms assignments images for help, and I stumbled upon some issues that
> I could not understand a proper (chemical) reasoning form them.
>
> Before the questions, let me just say I'm not implying there is any
> "bug" whatsoever: they are legitimate doubts from me. ;)
>
> Let's go:
> 1) Why ARG and LYS use atom type C8 instead of 2C? Because of the
> aminoacids side chain terminations with nitrogen atoms?
> 2) Why TRP and (all 3) Histidines use CT instead of 2C, given that in
> both cases the sp3 C atom is bonded to two "heavy" atoms?
> 3) Why GLU C_delta is 2C on X2 dihedral while it is defined as C on X3
> dihedral?
> 4) Why on both ASP and LEU the C_beta is 2C on X1 dihedral while it is
> defined as CS on X2 dihedral?
>
> Any (additional?) "chemical reasonings" for these are welcomed.
>
> 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 Sat May 25 2024 - 05:30:02 PDT
