Hi Erdem,
Dihedral potentials are a periodic function-- a sum of sine waves. The K
parameter controls the amplitude of the wave, but changing its sign is
equivalent to shifting the phase of the wave by 180 degrees. So, negative
potentials from paramfit *for dihedral terms only* are fine. If you don't
like the negative number, you can set the phase to 0 and it's the same
potential. Look at the AMBER equation or plot the potential function for
your dihedral of interest and it should make more sense.
Hope this helps,
Robin
On Thu, May 21, 2020 at 5:26 AM Erdem Yeler <erdemyeler.gmail.com> wrote:
> Hello,
> I parameterized some dihedrals with paramfit here is the result:
>
> oz-Z3-ob-ca 1 -1.2200 180.000 -1.000
> oz-Z3-ob-ca 1 4.2000 180.000 2.000
>
> AS you can see for the same dihedral one term has a negative Kn value
> (-1.2200) . Here, http://archive.ambermd.org/201602/0206.html Robin said
> "negative bond energy is a problem..." Actually in my case, there are 2
> terms for the same parameter but I hesitated about my parameters. is it a
> problem if one of the two terms for the same dihedral has negative energy?
> Can I use them? (By the way, minimized structure with this parameter was
> perfect: RMSD between minimized structure and X-ray experimental structure
> was 0.0003)
> Best regards,
> Erdem
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Received on Thu May 21 2020 - 15:00:02 PDT
