Dear Robin,
Thanks a lot for your response, it is really helpful.
Best regards,
Erdem
Robin Betz <robin.robinbetz.com>, 22 May 2020 Cum, 00:51 tarihinde şunu
yazdı:
> 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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> >
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Received on Sat May 23 2020 - 08:30:02 PDT
