what are the 4 atom types for this dihedral term? and did you make a list
of all of the sets of 4 atom types that surround this bond?
for the energy function, make sure to look at the information on the amber
web page
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
> > > > > > > _______________________________________________
> > > > > > > AMBER mailing list
> > > > > > > AMBER.ambermd.org
> > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > >
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
> > > > > > AMBER.ambermd.org
> > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 14 2022 - 08:30:03 PST
