Hello, I am trying to embed one chemical on another and have them fit as well as possible given the common substructure. I am (sometimes) having trouble with chiral centers. It’s automated, so I don’t want to hand-define things. The position restraints we introduce via ff.AddDistanceConstraint are usually working, but the hydrogen can sometimes get stuck on the “wrong” side of a carbon. Based on my previous experience with other molecular simulation tools, it’s the regular ff angle potentials that most strongly inhibit harmonic distance/position restraints from pulling the hydrogen over to the “correct”/desired side. What I would like to do is remove all angle potentials (or set their force constant to zero/near zero), do the EM via ff.Minimize(), then add back the regular angles and do EM again. However, I cannot figure out how to remove some or all of the regular ff potentials in python.
I investigated removing all bonds following this idea: https://github.com/rdkit/rdkit/issues/393 and generating a LJ/q-only force field, but the subsequent call to rdForceFieldHelpers.MMFFGetMoleculeProperties() returns None and then the AddDistanceConstraint() call fails. I also see that I can use rdkit.Chem.rdForceFieldHelpers.GetUFFAngleBendParams(), which works to print out what is there, but there does not seem to be an analogous Set function, at least not one that is accessible via python. Thank you for your advice, Chris.
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