I'll try to give you my thoughts on this, though there are many methods in
use.
IDIVF PK/6 PHASE PN
> O-CT-N-C 1 0.382890 108.00 -1.
>
it's not clear to me why you're dividing by 6.
> 1) It has been more than 10 years since I last parameterized a torsion
> angle right. To refresh my memory, Can an amber expert possibly confirm the
> general steps (outlined above) I took to derive the dihedral parameters.
>
it seems reasonable, but there are many ways to do this. You might look at
some of the papers, such as for the mdgx program, or paramfit, or our paper
on ff14sb (ff19sb is more complicated since it's 2D parameters).
>
> 2) In line of PN = -3, PHASE = -250.41, a negative PHASE value, does not
> sound right to me? Can it be replaced with (360 - 250.41 =) 109.59 ?
>
the phase is just a shift in the position of the minimum and it shouldn't
matter if you add 360 deg.
> 3) I have checked some amber FF parameters and I noticed some negative PK
> values. What is the rationale for negative PK values as energy barriers
> possess positive energies in difference PES curves after zeroing the lowest
> minimum energy point?
>
> a negative amplitude here just inverts that term in the Fourier series,
with a minimum instead of maximum. This could be done to reduce a barrier
that is too large. The same can be achieved with a different phase, so the
details will depend on how the fitting was done. The rationale can vary
depending on the protocol, but zeroing the lowest point isn't the only way
to approach the fitting, so it doesn't always work as you outlined above.
I would suggest redoing your grid scan to get energies using your new
parameters, and then making sure that the resulting energy profile is an
accurate match to your target profile. There are many ways it can go wrong
(such as forgetting the factor of 2 in the amplitude, or getting the units
wrong, or getting the divider wrong when you have multiple terms
contributing to the bond rotational energy, or other details of the
dihedral equation).
Thanks in advance for enlightening me.
>
> Best,
>
> Cenk Andac
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Received on Mon Feb 07 2022 - 14:00:02 PST
