Hi Baris!
Thank you for responding. I didn't know that 3D-NMR could measure energies
of dihedral angles. Can you pls suggest a research article for that?
I used paramfit because it comes with AMBER suite of packages and there is
a nice tutorial for it on amber website. Any other suggestions?
Huge energies, YES, that is what puzzles me. I still think I need to
optimize some parameters somewhere..I believe I need help at this point.
Best,
Cenk
On Thu, Sep 15, 2022 at 11:55 PM Barış KURT <peacewolfus09.gmail.com> wrote:
> paramfit deprecated anymore why are you still using it? Also your
> dihedrals' relative energies seems huge actually I don't think it is true.
> Did you check it experimentally? (with 3D NMR?)
>
> Cenk Andac via AMBER <amber.ambermd.org>, 15 Eyl 2022 Per, 23:46
> tarihinde şunu yazdı:
>
>> Dear Amber users,
>>
>> I applied paramfit to fit single-point rotational energies about a
>> dihedral
>> angle (of an nt derivative) determined by MM (blue plot in the figure),in
>> which Vn values for the dihedral were zeroed in the force field, to single
>> point QM energies (at the MP2 level) for the rotations about the same
>> dihedral angle (black in the figure). The red curve in the figure
>> represents the fit energies.
>> I used Shaw's RNA force field for parameterization.
>> I see that the energies obtained by MM is about 4 times as much as
>> energies
>> obtained by QM.
>> [image: image.png]
>>
>>
>> My question here is WHY?
>> Shouldn't they be about the same?
>>
>> Please see the plot below after dividing the MM energies by 4. Any ideas?
>>
>> [image: image.png]
>> best
>> Cenk
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Received on Sun Sep 18 2022 - 01:30:04 PDT
