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 - 08:30:03 PST
