Hi RDKitters, I'm having an issue using the MMFF to minimise a CORINA conformation. I've written a little script which adds hydrogens to a molecule then tries to use the MMFF forcefield to minimise the conformer. The problem is that the script hangs on the minimise step.
This error only occurs when I add hydrogens to the conformation, I assume the
reason for this is because the hydrogens are all added at the origin. Is there
a way of getting round this (in RDKit, as I want to keep the AddHs function)?
I've included the script below, it will work like this however if you switch
wrong the commented lines in the first for loop then the it no longer works.
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import ChemicalForceFields
from sys import argv
suppl = Chem.SDMolSupplier(argv[1])
molList = []
for mol in suppl:
#molList.append(Chem.AddHs(mol))
molList.append(mol)
del suppl
#w = Chem.SDWriter(argv[1])
w = Chem.SDWriter('test.sdf')
for mol in molList:
mp = ChemicalForceFields.MMFFGetMoleculeProperties(mol)
field = AllChem.MMFFGetMoleculeForceField(mol, mp)
field.Minimize()
w.write(mol)
w.close()
Thanks in advance.
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
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