Hello,
Hydrogen atoms bonded to oxygen atoms (type HO) do not have VDW radii
because it is assumed that it lies inside the VDW radius of the oxygen.
Other hydrogen atoms, i.e. bonded to nitrogen, have very small VDW radii to
prevent atoms from collapsing into one another (which does occasionally
happen in phosphate groups). I believe that the VDW terms for hydrogen
atoms NOT HO (or water h atoms) are primarily, if not exclusively,
repulsive.
You can see the VDW parameters at the end of the parm99.dat file in
$AMBERHOME/dat/leap/parm . You will see that only HO and HW (for water)
have 0.0000 as both VDW parameters.
Hope this helps,
Jason
On Tue, Aug 10, 2010 at 6:46 PM, Philippe Pinard <pp_amber17.yahoo.com>wrote:
> Hi Amber users
>
> Nonbond interactions (vdw, and electrostatics) in parm99 or gaff are the
> same.
> In Gaff paper it says concerning LJ (vdw), that:
> The van der Waals parameters of GAFF are as same as those used
> by the Amber parm94 or parm99 force fields. There is only one set
> of parameters (the internuclear separation of the ij pair at the
> potential minimum, r*ij, and the potential well, ij) for each element
> except hydrogen.
> What does "except hydrogen" mean? do they have or not corresponding vdw in
> there?
>
> Thanks in advance
>
>
>
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Aug 10 2010 - 18:00:03 PDT
