Dear Jan,
the origin of the difference is the different /nonBondedThresh/ default
value in |||MMFFOptimizeMoleculeConfs|(10.0) and in
|||MMFFGetMoleculeForceField| (100.0).
If you set /nonBondedThresh/ to 100.0 in
|||MMFFOptimizeMoleculeConfs|you indeed get the same value, as expected:
from rdkit import Chem
from rdkit.Chem import AllChem
smiles = "c1ccc(cc1)CCCCOCCCCCCNC[C@@H](c2ccc(c(c2)CO)O)O" #CONF_107
mol = Chem.MolFromSmiles(smiles)
mol = Chem.AddHs(mol)
m = Chem.Mol(mol)
confs = 20
AllChem.EmbedMultipleConfs(m, numConfs=confs,
randomSeed=2, useExpTorsionAnglePrefs=True,
useBasicKnowledge=True)
energies = AllChem.MMFFOptimizeMoleculeConfs(
m, maxIters=2000, nonBondedThresh=100.0)
energies_list = [e [1] for e in energies]
min_e_index = energies_list.index(min(energies_list))
#print(energies_list)
print(energies_list[min_e_index])
62.445185999826535
mol.AddConformer(m.GetConformer(min_e_index))
prop = AllChem.MMFFGetMoleculeProperties(mol, mmffVariant="MMFF94")
ff = AllChem.MMFFGetMoleculeForceField(mol,prop)
low_energy = ff.CalcEnergy()
print(low_energy)
62.445185999826535
Cheers,
p.
On 12/06/18 19:31, Jan Halborg Jensen wrote:
The following code gives
63.50505459068998
66.40551367349616
I don’t understand why the two numbers are not the same
Any tips would be appreciated
Thanks, Jan
smiles = "c1ccc(cc1)CCCCOCCCCCCNC[C@@H](c2ccc(c(c2)CO)O)O" #CONF_107
mol = Chem.MolFromSmiles(smiles)
mol = Chem.AddHs(mol)
m = Chem.Mol(mol)
confs = 20
AllChem.EmbedMultipleConfs(m,numConfs=confs,randomSeed=2,useExpTorsionAnglePrefs=True,useBasicKnowledge=True)
energies = AllChem.MMFFOptimizeMoleculeConfs(m,maxIters=2000)
energies_list = [e[1] for e in energies]
min_e_index = energies_list.index(min(energies_list))
#print(energies_list)
print(energies_list[min_e_index])
mol.AddConformer(m.GetConformer(min_e_index))
prop = AllChem.MMFFGetMoleculeProperties(mol, mmffVariant="MMFF94")
ff = AllChem.MMFFGetMoleculeForceField(mol,prop)
low_energy = ff.CalcEnergy()
print(low_energy)
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