Hi,
a similar question has come up recently on the RDKit mailing list:
https://www.mail-archive.com/rdkit-discuss@lists.sourceforge.net/msg08995.html
the GetUFFVdWParams() and GetMMFFVdWParams() functions will return the
vdW parameters for UFF and MMFF94 force fields, respectively. For UFF
the function indeed returns sigma and epsilon van der Waals parameters
for atoms with indexes idx1, idx2 as a (x_ij, D_ij) tuple, as per the
vdW functional form in UFF:
However, for MMFF94, as explained in the link reported above, the
parameters returned by
GetMMFFVdWParams() are not quite sigma and epsilon as the vdW term uses
a different 14-7 term with combination rules which depend on the
chemical nature of the two particles.
Cheers,
Paolo
On 07/08/19 07:25, Masgils wrote:
Hi, All
I want to calculate Lennard-Jones potential between a small molecule
probe and a atom. How do I get the sigma and epsilon parameters by
using rdkit?
{\displaystyle {\mathcal {V}}\left(r\right)=4\varepsilon
\left[\left({\frac {\sigma }{r}}\right)^{12}-\left({\frac {\sigma
}{r}}\right)^{6}\right]}
Best Regards,
M.
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