On Fri, Mar 30, 2012, setyanto md wrote:
>
> I read in AmberTool 1.5 manual in the section of "specifying a force field".
>
> In section 2.2 The ff10 force field, said "*The ff10 force field collects a
> variety of updates and modifications to the (generally rather successful)
> ff99 force field*"
>
> and in the section 2.4 The Duan et al. (2003) force field, said "*The ff03
> force field [19, 20] is a modified version of ff99 (described below). The
> main changes are that charges are now derived from quantum calculations
> that use a continuum dielectric to mimic solvent polarization, and that the
> φ and ψ backbone torsions for proteins are modified, with the effect of
> decreasing the preference for helical configurations*"
>
> Both forcefield (ff10 and ff03) was based on ff99. But in ff03, it was
> explained the main changes, while in ff10 it is only tell a variety of
> updates.
Seems to me you are not looking carefully at the rest of section 2.2, which
describes in a fair amount of detail how ff10 differs from ff99. To get more
info, you'll have to read the papers that are cited.
> 4. I will make simulation of enzyme molecule in water and also some
> non-aqueous solvent at some different temperature. Which one is better for
> me to use the forcefield ? ff10 or ff03.
None of the Amber force fields have been calibrated or tested for such
calculations.
....dac
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Received on Fri Mar 30 2012 - 09:30:04 PDT
