they are available for download on the amber web site (www.ambermd.org),
along with a lot of information on the format. make sure to compare energies
and forces from your code to that from Amber- there are multiple examples in
the past of people using "Amber" force fields, but not doing the conversion
or calculation correctly.
On Mon, Mar 15, 2010 at 8:46 AM, <whimsica.aol.com> wrote:
>
> I'm writing a small molecular dynamics system for students and would like
> to try using amber forces in a simulation.
> On wikipedia it says that the amber force field can be calculated using
>
>
>
>
>
>
>
>
> and the parameters of the force field (e.g. force constants, equilibrium
> bondlengths and angles, charges). Peptide, protein and nucleic acid
> parameters are provided byparameter sets with names beginning with "ff" and
> containing a twodigit year number, for instance "ff99"
>
> Could someone please point me to the parameter file(s) that would including
> everything necessary to use this equation.
> I'm writing a small molecular dynamics system for students and would like
> to try using amber forces in a simulation.
>
> Thanks,
>
> Daniel Savage
> CinematicSciences
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Mar 15 2010 - 08:00:02 PDT
