>I have already assigned extra PNs as negative.
My question was rather about negative Vn/2/x values.
Dear Cenk, sorry for misunderstanding. I think you used paramfit or mdgx
for parameterization. Negative Vn/2 values are fine but if you don't want
to use them just set the phase. (Maybe somebody has already answered this
question too but I answered just in case..)
Regards,
Cenk Andac <cenkandac.gmail.com>, 14 Şub 2022 Pzt, 19:59 tarihinde şunu
yazdı:
> 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 - 10:30:02 PST
