it depends a lot on what kind of experimental data you have, and whether
you'll have it packed in a binding pocket (maybe nonbonded is most
important), or if it can be flexible where you'll need to worry about
dihedral accuracy as well.
On Thu, Dec 21, 2023 at 1:59 PM Matthew Guberman-Pfeffer via AMBER <
amber.ambermd.org> wrote:
> Dear Amber Community,
>
> I want to compare different sets of parameters for a cofactor to tell if
> they are equivalent or if one should be preferred. I can run one simulation
> with each set of parameters and compare the RMSDs, but would that be
> statistically meaningful? Is there a better approach for assessing the
> quality of forcefield parameters? Here I specifically have in mind
> comparing two different sets of charge distributions depending on, for
> example, the number or type of conformers included in RESP-fitting.
>
> I’d greatly appreciate your advice!
>
> Best,
> Matthew
>
>
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Received on Thu Dec 21 2023 - 13:00:02 PST
