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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> > >
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Received on Mon Feb 14 2022 - 01:30:03 PST
