Forgot to name the dihedral angle.
It is O4'C1'N1C6 of a pyrimidine nucleotide.
It is hard to type in on my way home.
Sorry for several messages to answer your questions.
Best
On Monday, February 14, 2022, Cenk Andac <cenkandac.gmail.com> wrote:
> Hi Prof. Simmerling,
> Thank you for responding.
> My compound is a nucleotide derivative. And I am particularly interested
> in kappa dihedral angle between C1' (of ribofuranosyl ring) and N1 (of a
> pyrimidine derivative I synthesized in my laboratory).
>
> "a negative amplitude for the cosine term"
> As if
> For positive amplitude
> y=a.cos(bx)
> and for negative amplitude
> y=(-a). cos (bx)
>
> Is that right?
>
>
> Regards,
> Cenk
>
>
> On Mon, Feb 14, 2022, 6:41 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> I am not sure why you are dividing by 6 - maybe it would help if you can
>> describe the molecule and the atoms/atom types that surround the rotatable
>> bond for these parameters.
>>
>> a negative amplitude for the cosine term just makes that function have a
>> minimum where it would otherwise have a maximum. This could be used to
>> reduce a barrier that is too igh (for example, there are other reasons to
>> do this, and it also can be done other ways).
>>
>> On Mon, Feb 14, 2022 at 10:19 AM Cenk Andac <cenkandac.gmail.com> wrote:
>>
>> > Hi Barış ,
>> >
>> > Thank you for responding.
>> > That sounds more like periodicity (PN) you are talking about.
>> > I have already assigned extra PNs as negative.
>> > My question was rather about negative Vn/2/x values.
>> >
>> > Best,
>> >
>> > Cenk
>> >
>> > On Mon, Feb 14, 2022 at 12:23 PM Barış KURT <peacewolfus09.gmail.com>
>> > wrote:
>> >
>> > > Dear Cenk,
>> > > negative value means there are more than one dihedrals... and divide
>> 6
>> > > means two atoms sees each other 6 times when you rotate them (360). In
>> > > amber manual this subject explained in details. By the way, sometimes
>> you
>> > > will need a novel atom types (if you are not using gaff/gaff2). Please
>> > see
>> > > my articles ...
>> > > Regards,
>> > >
>> > >
>> > > Cenk Andac <cenkandac.gmail.com>, 14 Şub 2022 Pzt, 12:10 tarihinde
>> şunu
>> > > yazdı:
>> > >
>> > > > Dear Prof. Simmerling,
>> > > >
>> > > > Thank you for your response and indispensible info you provided.
>> > > >
>> > > > 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.
>> > > > >
>> > > >
>> > > >
>> > > > > >(such as forgetting the factor of 2 in the amplitude, or getting
>> the
>> > > > units
>> > > > > wrong,
>> > > >
>> > > >
>> > > > Well, I have thought PK would equal to half the potential energy at
>> the
>> > > > energy barrier [PK=(V2)/2]. That is
>> > > > indeed what I did. PK/6 indeed means (V2)/2/6 as I have stated that
>> in
>> > > my
>> > > > previous message as follows
>> > > > "Instead, I took half the max potential-energies at the barriers and
>> > > > divided them by 6".
>> > > > I guess, I should have formulated my statement before for
>> > clarification ,
>> > > > PK=(V2)/2.
>> > > > Overall, I actually divided the potential energy at the barrier by
>> 12
>> > > (V2 /
>> > > > 12).
>> > > > Sorry for keeping you in dark for not providing the real
>> equilibration
>> > I
>> > > > used.
>> > > >
>> > > > Is that what you were wondering? I would appreciate it much if you
>> > could
>> > > > confirm the equilibration above?
>> > > >
>> > > > > a negative amplitude here just inverts that term in the Fourier
>> > series,
>> > > > >with a minimum instead of maximum.
>> > > >
>> > > > That sounds interesting. I am currently doing a production run
>> > simulation
>> > > > with the current parameters I found.
>> > > > But, I also would like to try inverting the Fourier series for a
>> > minimum.
>> > > > I am kind of in dark here though as I have not tried that before.
>> > > > What do you mean exactly by "with a minimum"? Would that be the
>> minimum
>> > > > points right around the maximum point at the barrier ?
>> > > > How would one invert the Fourier series?
>> > > >
>> > > > >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).
>> > > >
>> > > > I have looked at the ff19sb paper of yours. Well, that looks quite
>> > > > advanced. Optimization of parameters
>> > > > using a GRID model is quite interesting. It would be nice to learn
>> that
>> > > > algorithm for force field development.
>> > > > How did you actually generate the GRIDs , using cpptraj or
>> GAMESS-US?
>> > > >
>> > > > Regards,
>> > > >
>> > > > Cenk Andac
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > > On Tue, Feb 8, 2022 at 12:55 AM Carlos Simmerling <
>> > > > carlos.simmerling.gmail.com> wrote:
>> > > >
>> > > > > 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.
>> > > > >
>> > > >
>> > > >
>> > > > > (such as forgetting the factor of 2 in the amplitude, or getting
>> the
>> > > > units
>> > > > > wrong,
>> > > > >
>> > > > > > 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 14 2022 - 09:00:03 PST
