Hi Robin,
just following up because I also misunderstood when I first read this
paper, but I think I eventually understood. You didn't take the QM energies
and recover the ff99SB parameters by optimizing the QM-MM difference, but
instead you used the ff99SB energy profile and showed that you can find
what parameters produce the specific MM energy profile, right? I think
that's what you're saying above but I just wanted to make sure I
understood.
cheers
carlos
On Tue, Jan 24, 2017 at 2:35 PM, Robin Betz <robin.robinbetz.com> wrote:
> Hi Stefano,
>
> In the paper I started with tetraalanine parameterized with the ff99
> forcefield, and fit the phi and psi dihedrals to ff99SB energies. However,
> ff99 has only 2 dihedral terms for phi/psi, while the ff99SB correction has
> more. So I created a prmtop with those extra dihedral terms present and set
> the force constants all to 1, as Paramfit doesn't care about the initial
> value for a term.
>
> The only difference between ff99 and ff99SB is the phi and psi terms, so it
> doesn't really matter either way. To verify, check parm99.dat (ff99) vs
> frcmod.ff99SB and you'll see only phi and psi terms are redefined.
>
> This test case in the paper is more of a proof of concept of Paramfit's
> functionality, showing that it can fit "apples to apples" and can recover
> constants in the AMBER equation from energies generated with that same
> equation. It's much harder to demonstrate that a program will always
> generate the best fit to QM energies, as the AMBER equation provides a
> Newtonian approximation of systems that are really governed by quantum
> rules.
>
> Hope this helps,
> Robin
>
> On Tue, Jan 24, 2017 at 11:07 AM, BOSISIO Stefano <s1374284.sms.ed.ac.uk>
> wrote:
>
> > Dear Amber staff,
> >
> >
> > I am struggling a bit to use Paramfit to reproduce the exact
> > dihedrals'amplitudes values of ff99SB forcefield for tetraalanine as
> > written in Paramfit paper (10.1002/jcc.23775) .
> >
> > In particular, I cannot understand if you started with a tetraalanine
> > parametrized with ff99 force field ( with Phi and Psi amplitudes set to
> > 1.0 ) and then fitted it to ff99SB, or if you started with ff99SB (with
> Phi
> > and Psi amplitudes set to 1.0 ) and fitted it to the real ff99SB.
> >
> >
> > Thank you very much,
> >
> >
> > Best wishes,
> >
> > Stefano
> >
> >
> > The University of Edinburgh is a charitable body, registered in
> > Scotland, with registration number SC005336.
> >
> > _______________________________________________
> > 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 Tue Jan 24 2017 - 13:00:02 PST
