Hi Stefano,
> I would like to ask a question on NON Bond parameter of GAFF and on
> AMBER force field.
>
> I have not a clear idea on how no bond vdw parameter work.
>
> For example in the "gaff.dat" file at the bottom there are four column
> that begin with:
>
>
> MOD4 RE
>
> h1 1.3870 0.0157 Veenstra et al JCC,8,(1992),963
> h2 1.2870 0.0157 Veenstra et al JCC,8,(1992),963
> ho 0.0000 0.0000
> ...
> END
>
> 1) How is the right mening of these parameter?
These, I believe, correspond to the atom symbol, the VDW radius (in
angstroms) and the 6-12 well depth in kcal/mol. Note there are two ways to
specify the VDW parameters based on the presence of the keyword RE or AC. If
it is RE as you have here then you specify VDW radius and well depth. If it
is instead AC then it would be the A and B coefficients (A/R^12, B/R^12).
More details (although possibly slightly cryptic) are here:
http://ambermd.org/formats.html#parm.dat
> 2) Why the atomtype 'ho' has both zero parameters?
This follows the approach used in the FF9X force fields (and TIP3P) whereby
hydrogen's bonded to Oxygens have zero VDW radii. The same approach is used
in GAFF. Essentially the H atom is considered to be completely enclosed
within the Oxygen VDW radius. Some force fields, notably CHARMM include a
very small VDW radii on such H's to avoid problems in very polarized
systems, such as phosphates where the H can collapse onto the phosphorus and
cause problems.
I hope this helps.
All the best
Ross
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|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
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Received on Tue Oct 20 2009 - 12:00:03 PDT
