On Tue, Mar 08, 2022, Nathan Black wrote:
>
>IMPROPER
>CX-O2-C -O2 10.5 180.0 2.0 Using general improper
>torsional angle X-O2-C-O2, penalty score= 3.0
>
>Can anyone with more experience tell me how significant of a penalty score
>this is, and if it is worth trying to fix using paramfit or mdgx?
As the comment in the parmxx.dat files indicate, this out-of-plane penalty
for the C in a CO2 group was established in 1986(!), and no one has touched
it since then. It keeps the four-atom group planar with a pretty strong
restraint. There is no evidence that anyone has thought about this in some
four decades; for example, the GAFF force field just took this parameter
over from the same source.
>because this parameter is also missing for standard amino acid residues,
>and not just the nonstandards that I built myself.
This is a "wild-card" because the thought is that the CO2 group planarity is
independent of the atom type the carbon is bonded to.
I'd personally think that there are lots of other things of higher priority
in force field development for non-standard amino acids.
....dac
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Received on Wed Mar 09 2022 - 06:30:02 PST
