AMBER Archive (2008)

Subject: Re: AMBER: parameters of nonbonded potentials

From: David A. Case (case_at_scripps.edu)
Date: Tue Feb 19 2008 - 10:05:07 CST

On Tue, Feb 19, 2008, Alexander Klenner wrote:
>
> I am trying to implemt the General Amber Forcefield (Gaff) using the
> equation given in Junmei et al 2003. I already found all the parameters
> for bonds, angles and dihedrals in the gaff.dat of the antechamber archiv.
>
> My question is, wether the paramters Aij Bij qi qj have to be
> calculated for every pair of atoms or if there is a possibility to read
> them from a parameter file and if so where can I find them?

If you use Amber or NAB, the prmtop file contains the parameters needed for
the particular system in question. These are computed from the parameters
given in the gaff.dat file.

So, if you are implementing your own version, I think you will need to do
something similar. Note that Aij and Bij depend on a small number of atom
types; the charges need to be calculated (by a quantum chemistry procedure)
for every molecule.

...good luck....dac

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