Date: Wed, 7 Sep 2022 21:55:07 +0300
Hi again, As I have moveed along the paramfit tutorial, I saw the
following equation, which I think already answers my question.
[image: image.png]
best,
Cenk
On Wed, Sep 7, 2022 at 3:38 PM Cenk Andac <cenkandac.gmail.com> wrote:
> Hi Erdem,
> thanks for correcting the energy term in the eq. the equation should have
> been
>
> EMMdihedral = (PK/IDIVF) * (1 + cos(PN*phi – PHASE)) EQ.1
>
> and the EQM energy is rectified (EQMr) by substracting EMM (computed by zeroing Vn parameters for the dihedral of interest) from EQM to
> yield a a final EQMr curve , to which we fit the EMM curve.
> EQMr= EQM - EMM(with zero dihedral parameter of interest) EQ.2
>
> Having said that, my question was
>
> whether or not QM potential energies computed by paramfit are rectified by EQ.2.
>
> If not, do we need to rectify it manually? or Do we really need to rectify it as in EQ.2.
>
> best,
>
> Cenk
>
>
> On Wed, Sep 7, 2022 at 12:51 PM Erdem Yeler <erdemyeler.gmail.com> wrote:
>
>> I think you are confused : in quantum_A.dat, you should put quantum
>> energies not MM energies. (PK/IDIVF) * (1 + cos(PN*phi – PHASE)) is a MM
>> energy NOT QM Energy.
>> All the best,
>> Erdem
>> Istanbul Technıcal University
>> Department of Chemistry
>>
>>
>>
>> Cenk Andac via AMBER <amber.ambermd.org>, 6 Eyl 2022 Sal, 18:16
>> tarihinde şunu yazdı:
>>
>>> Dear Amber community,
>>>
>>> I have been working on dihedral parameters development using paramfit.
>>> I have a simple question.
>>> In developing AMBER dihedral parameters the following EQ is used.
>>>
>>> Edihedral = EQM - EVDW-ELE(MM) = (PK/IDIVF) * (1 + cos(PN*phi – PHASE))
>>>
>>> here
>>> Edihedral = EQM - EVDW-ELE(MM)
>>>
>>> I was wondering when running paramfit with -q quantum_A.dat
>>>
>>> what kind of QM energies I need to use in
>>> quantum_A.dat, Edihedral or EQM ?
>>>
>>> thanks in advance,
>>>
>>> best
>>>
>>> Cenk Andac
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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