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
>
>
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> Scotland, with registration number SC005336.
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Received on Tue Jan 24 2017 - 12:00:03 PST
