Hi there folks,
Using RDKit 2010_12_1.
Can someone explain why almost none of my molecules are ever successfully
minimized?
I know I can play around with the values of maxIts, forceTol and energyTol,
but I was trying to avoid that if possible.
Should I throw away the structures which are not minimized? My impression,
from examining RMS values to the original structure before and after the
minimization step , is that some form of minimization still occurs - even if
the Minimize() function returns 1.
Example code:
from rdkit import Chem
from rdkit.Chem import AllChem
mol =
Chem.MolFromSmiles('Cc1c(C(C2CC2)N2CC(C3CCCN(C(=O)OC(C)(C)C)C3)c3ccccc32)cccc1')
mol_h = AllChem.AddHs(mol)
cids = AllChem.EmbedMultipleConfs(mol_h, numConfs=50)
for cid in cids:
ff = AllChem.UFFGetMoleculeForceField(mol_h, confId=cid)
print ff.Minimize()
Can anyone shed some light?
-
Jean-Paul Ebejer
Early Stage Researcher
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