Hi Chris, you can switch on/off individual MMFF potential terms in the force field; you can't do that with UFF. To switch off all angle terms in MMFF you can do the following:
from rdkit import Chem, ForceField from rdkit.Chem import rdForceFieldHelpers mp = rdForceFieldHelpers.MMFFGetMoleculeProperties(mol) mp.SetMMFFAngleTerm(False) ff = rdForceFieldHelpers.MMFFGetMoleculeForceField(mol, mp) ff.Minimize() Then, to do another minimization with all terms on, you will need to re-create a complete force field: mp.SetMMFFAngleTerm(True) ff = rdForceFieldHelpers.MMFFGetMoleculeForceField(mol, mp) ff.Minimize() If you detect an H atom stuck on the wrong side of a tetrahedral center you might also consider inverting its direction vector with respect to the C atom it is bonded to before minimizing. HTH, cheers p. On Fri, Jun 25, 2021 at 2:10 AM Neale, Christopher Andrew via Rdkit-discuss <rdkit-discuss@lists.sourceforge.net> wrote: > 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. > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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