>
> Oh by the way!
>
> The equation below is exactly what I used to determine PHASE.
>
> Best ,
> (PK/IDIVF) * (1 + cos(PN*phi - PHASE))
>
>
> https://ambermd.org/FileFormats.php
>
> search for "INPUT FOR DIHEDRAL PARAMETERS" and read the information about
> the parameters and the equation. It's different from what you listed.
>
>
> On Mon, Feb 14, 2022 at 11:23 AM 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
