Thank you very much Paolo! That worked technically but did not accomplish what I was hoping it would. What ended up working was looping through the common core and setting the target x,y,z coordinates to the reference coordinates prior to the energy minimization.
Thank you again, Chris. From: Paolo Tosco <paolo.tosco.m...@gmail.com> Date: Friday, June 25, 2021 at 1:57 AM To: "Neale, Christopher Andrew" <cne...@lanl.gov> Cc: "rdkit-discuss@lists.sourceforge.net" <rdkit-discuss@lists.sourceforge.net> Subject: [EXTERNAL] Re: [Rdkit-discuss] How can I remove all angle potentials from a force field before EM? 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<mailto: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<mailto:Rdkit-discuss@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
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