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
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