[Rdkit-discuss] Peptide cis/trans bonds

[Bruce M. <bf...@gm...>]

Hi,

Does anyone know how I can force RDKit to keep peptide bonds ‘trans’ during conformer generation and subsequent minimisation? The structures will be used for docking so the absolute quality of the geometries is not so much an issue but I’d like to avoid glaringly awkward things like these cis-peptide bonds.

The procedure I’m using is basically:

m = Chem.MolFromMolFile(f, sanitize=True, removeHs=False) # Using a .mol file with hydrogens already added.

confIds = AllChem.EmbedMultipleConfs(m, numConfs=10,
                                     clearConfs=False,
                                     useRandomCoords=True,
                                     enforceChirality=True,
                                     useExpTorsionAnglePrefs=True,
                                     useBasicKnowledge=True,
                                     numThreads=0)

for id in confIds:
    AllChem.MMFFOptimizeMoleculeConfs(m, numThreads=0, mmffVariant='MMFF94', confId=id)
    print >>file('{0}{1}.mol'.format('conformer_', count), 'w+'),Chem.MolToPDBBlock(m, confId=id)
    count += 1

Cheers,
Bruce Milne