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 rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import rdmolops
mols = Chem.SDMolSupplier('test_3c.sdf')
for mol in mols:
# UFF
ffu = AllChem.UFFGetMoleculeForceField(mol)
energy_value_U = ffu.CalcEnergy()
print(energy_value_U)
# MMFF
mol = rdmolops.AddHs(mol, addCoords = True)
mp = AllChem.MMFFGetMoleculeProperties(mol)
ffm = AllChem.MMFFGetMoleculeForceField(mol, mp)
energy_value_M = ffm.CalcEnergy()
print(energy_value_M)
My problem is that I get weird energy values (not all the time I think, but
too often). Either too high or too low. And i don't get why.
I would like to get the energy of my ligand as he is. Without changing it's
conformation at all. That's why I don't use the minimization function, or
optimization. First I also didn't add the hydrogen, but thanks to one of
Paolo Tosco's code (mmffEnergyTerms.py), I saw that H are not included even
if they are in the sdf file. But, I still have some weird values i think.
Here three examples:
GNP_1CIP : -305.2896 kcal/mol (MMFF, with H added)
-46.4812 kcal/mol (MMFF, without H add)
278.6606 kcal/mol (UFF)
SAM_2IGT: 1675.9951 (MMFF, with H added)
151.6481 (MMFF, without H add)
217.1217 (UFF)
ACP_3A1C: 222.9396 (MMFF, with H added)
269.151 (MMFF, without H add)
217.1217 (UFF)
Regards,
Méliné
test_3c.sdf
Description: Binary data
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