Bill,
Thanks for the link. As far as I understood, the vdw parameters r* and e
are calculated in a particular way in AMBER force field such that the
TIP3P oxygen is the 'reference' element/atom type in the vdw
parameterization of cations. I am trying to convert some of the parameters
from a paper (Langmuir 20, 3138, 2004) to AMBER format and would like to
ask some question:
The vdw energies in that paper is calculated using the following equation:
E_vdw = D0 * [(R0/R)^12 - 2(R0/R)^6].
And for sulphur (S), the vdw parameters are D0=0.25 kcal/mol and
R0=3.98744 A. These parameters are from FFII force field, according to the
paper.
The equation representing AMBER vdw energy is similar to the following
equation (defined in
http://ambermd.org/Questions/vdw.html)
E_vdw_amber = e * [(r*_ij/r)^12 - 2 * (r*_ij/r)^6]
but r*_ij is not what is defined in the AMBER .dat files, which is I think
the crucial point here. For example, R0 for S is 3.98744 A in FFII, but if
I want to use these parameters in the AMBER format, I have to set r* for S
to be 3.98744/2, not 3.98744, is this right?
R0 is the interatomic distance between two atoms while r* has a different
meaning. If the atom type in interest is a cation, r* is [ (minimum energy
distance) - 1.768 ] (which is the vdw radius of oxygen in TIP3P water). If
the atom in interest is not a cation, then it represent (minimum energy
distance)/2. Thanks again.
Best regards,
PS: Jason, thanks for the .pdf file.
Ilyas Yildirim, Ph.D.
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-----------------------------------------------------------
On Mon, 4 Oct 2010, Bill Ross wrote:
> Here is more on the L-J formulas:
>
> http://ambermd.org/Questions/vdw.html
>
> Bill
>
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>
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Received on Mon Oct 04 2010 - 17:30:04 PDT
