This issue is far from being trivial.
To address the question, I recommend looking at this simple example
(attached pdf file) which shows that even when the atom distance is twice
the vdw diameter, there is still attraction between atoms (unified type,
with
implicit H atoms).
Some, but not all, consider that water screens out interactions, that
is, the
vdw interaction is attractive provided that R < Rm + 2 x R(H2O).
But then, one may also need to consider the special case of water-mediated
H-bonds, where the heavy atoms being considered are polar.
HTH,
Nadir
Pr. Nadir T. Mrabet
Cellular & Molecular Biochemistry
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Clayton, Gina Martyn wrote:
>
> Hi CCP4ers
>
> Perhaps I am hashing over old news…..but
>
> We are having a discussion about Van Der Waals contacts and effective
> contacts i.e. the "real distance" of a VDW bump between say a CH and a
> CH group which sometimes is described as between a C and a C as i.e.
> 2x 1.6A and ending about 4A but not including hydrogen.
>
> Some programs list contacts, to say a ligand, as far as 6A apart and
> some of the simulation programs use that distance too for contacts for
> protein protein interactions.
>
> Does anyone know of a good paper that discusses the effective distance
> or has a comment on where a VDW force may begin and end or it's
> effective distance - though some say it never truly ends just
> approaches zero...
>
>
> G
>
>
>
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