On Mon, Mar 25, 2013 at 8:12 AM, Anna MARABOTTI <amarabotti.unisa.it> wrote:
>
>
> Dear Amber users,
>
> I am new to this list, and I am not currently
> using Amber. I'd need an help to understand a problem that I have with
> Antechamber suite.
>
> I want to calculate parameters for a cofactor of a
> green fluorescent proteins, using Amber99SB ff, in order to implement
> these parameters into the ff used by GROMACS. I used Antechamber to
> perform calculations, following the Antechamber tutorial. I obtained the
> .mol2, .frcmod, .prmtop and .inpcrd files regularly.
>
> To implement
> these parameters into the Amber99sb forcefield, I have to convert them
> since the units are not equal: in the .frcmod I understand that, e.g.
> the bond force constant is expressed in kcal/(mol A^2), whereas in the
> parameters set in the AMBER99SB forcefield for GROMACS, the force
> constant is expressed in KJ/(mol nm^2). Therefore, roughly to convert my
> Amber parameters into Gromacs parameters, I should multiply them by
> approx. 418.4.
>
> I checked the parameters present in both files, and I
> see that the difference is not approx. 400, but approx. 800. I don't
> understand what is the source of this factor of 2. I obviously asked the
> same to GROMACS users, but I'm checking also with you. Are parameters in
> .frcmod file referred only to one atom, or to both (so I have to
> multiply - or divide - by 2)?
>
I think the difference is that the parameter in the Amber force field files
is k from the equation
E_bond = k(x-x0)^2
whereas in the GROMACS force fields, the force constant is k from the
equation
E_bond = 1/2 k (x-x0)^2
which is the more classical version of Hooke's law since 'k' is the actual
stiffness of the oscillator.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Mar 25 2013 - 06:00:04 PDT
