Hi Lewis,
The reason why it takes two particle indices as input is that MMFF94
uses rather complex combination rules for the van der Waals term.
In particular, EvdW between two particles /i/ and /j/ is given by the
following equation:
where /R/_/ij/ is the distance between particles /i/ and /j/, while
/R/_/ij/^* and /ε//_ij / are constants computed through these equations:
/B/ is 0 if one of the particles is a HBD, otherwise it is 0.2, while
the expression for /γ/ is:
This is the reason why you need to pass two particles to get the values
of /R/_/ij/^* and /ε//_ij /: you need to know if either particle is a
HBD to compute /R/_/ij/^* , and /ε//_ij / depends on R_/ij/^* .
Finally, if /i/-/j/ is a HBD-HBA interaction, R_/ij/^* is further scaled
by the factor DARAD = 0.8, while /ε//_ij / (which is computed using the
unscaled R_/ij/^* ) is scaled by the factor DAEPS = 0.5.
More information is available on the MMFF94 paper by Thomas A. Halgren
which describes the non-bonded terms:
Merck molecular force field. II. MMFF94 van der Waals and electrostatic
parameters for intermolecular interactions
<https://doi.org/10.1002/(SICI)1096-987X(199604)17:5/6%3C520::AID-JCC2%3E3.0.CO;2-W>
Cheers,
p.
On 03/07/2019 03:24, Lewis Martin wrote:
Hi all,
Can anyone please help explain what values are returned
by GetMMFFVdWParams? It takes two indices as input, so is it an
interaction term between the two? Or is it the well depth and minimum
(i.e. epsilon and R)?
Example:
In:
m = Chem.MolFromSmiles('C1CCC1OC')
m2=Chem.AddHs(m)
AllChem.EmbedMolecule(m2)
AllChem.MMFFOptimizeMolecule(m2)
pyMP = AllChem.MMFFGetMoleculeProperties(m2)
pyFF = AllChem.MMFFGetMoleculeForceField(m2, pyMP)
pyMP.GetMMFFVdWParams(0,1)
Out:
(3.9377389919289634,
0.06779699304291371,
3.9377389919289634,
0.06779699304291371)
The code at
https://github.com/rdkit/rdkit/blob/master/Code/ForceField/Wrap/ForceField.cpp
says it returns R_ij_starUnscaled, epsilonUnscaled, R_ij_star, and
epsilon, but Im unclear on what the scaling is or why two indices are
needed.
Thanks!
lewis
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