>> 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.
>
> It seems you can't have E_vdw for only 1 atom. Perhaps this is for S-S?
The parameters for S is D0=0.25 and E0=3.98744, so yes, I would assume
that the E_vdw with these numbers would represent the S-S vdw energy.
>> 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?
>
> Amber has R*i for each atom type in the .dat file.
> R*ij is for a pair of atom types.
> Usually a given R*i should work for that atom i combined with
> any other atom type j. However, for water params that involve
> a single large vdw on O to enclose H's too, one needs to come
> up with a R*i for the ion that allows for this. (Note that ion
> params derived like this do not make sense for combining with
> ordinary atoms, hence ions embedded in solute should ideally
> have different vdw from the same ion in water.)
>> R0 is the interatomic distance between two atoms
>
> I think it's the _equilibrium_ distance between 2 atom types.
Yes, sorry for this mistake. It is the distance between 2 atoms when
energy is at minimum.
>> while r* has a different meaning.
>
> I'm suspecting R*ij = R0, maybe if type i == type j.
When i=j, R0 is the equilibrium distance for this atom type. Except ions,
the vdw parameters defined in a force field for an atom type basically
comes from interatomic distance vs energy curve of the same two atoms.
When energy is minimum, that distance R0 represents the equilibrium
distance. In some force field like the one above, one of the parameter is
this R0. In AMBER, however, R0/2=r* is defined in the .dat force field
file for an atom type (which is not an ion). When vdw energy between
different atom type are calculated in the above ff, R0_ij = (R0_i+R0_j)/2,
where R0_i and R0_j are the vdw parameters of atom types i and j,
respectively. In AMBER, r*_ij = (r*_i+r*_j), I think. The well depth,
e_ij, for 2 different atom types are mixed as sqrt(e_i * e_j) in both the
above ff and AMBER ff.
I guess when someone needs to convert the vdw parameters from one force
field to AMBER, this recipe should be followed. The key point is to
subtract the vdw radius of O from r*_ij to find the vdw parameter r*_i of
an ion. For other atom types, r*_i = r*_ii/2. The link you provided in
your previous email was very useful, thanks.
Best regards,
Ilyas
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Received on Mon Oct 04 2010 - 19:30:03 PDT
