Dear Méliné,
if you wish to keep input hydrogens you need to add a "removeHs = False"
parameter to Chem.SDMolSupplier(); hydrogens are removed by default.
As Peter pointed out, the original coordinates may give large energy
values just because of small deviations from ideal values of bond
Small atomic displacements can cause large forcefield energy differences.
Computing molecular-mechanics energies from exactly the same coordinates
using two different force-fields is probably not a reasonable procedure.
It would be better to do an energy minimization with the two force fields
Dear all,
I'm still a beginner with Rdkit, and I’m having a hard time calculating the
energy of conformers.
I think I have read all the topics on the subject, but I might have missed
something.
Here is a shorten version of a code I wrote thanks to all the information I
could find here.
from
3 matches
Mail list logo
