There shouldn't be any expectation that the MMFF energy should converge to
1kcal/mol.
There *may* be a case to be made for the MMFF_energy - Global_minimum be <
1kcal/mol, however, in general, we don't know what the global minimum is.
I suggest looking at this paper:
The code below shows the lowest energy found for 6 different protomers defined
by the smiles strings below as a function of number of conformers. Even with
2000 conformers I am not getting convergence to within 1 kcal/mol for
comp109_1=2.
Is this expected? Any advice or tips appreciated
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