Re: [Rdkit-discuss] mmFF minimization in context of two ligands/binding pocket

Dear Steven, just to add up a small bit to Maciek's reply, you may find some examples how to use the RDKit MMFF94 C++ API in Code/ForceField/MMFF/testMMFFForceField.cpp and in Code/ForceField/MMFF/testMMFFHelpers.cpp. All of the constraints are available from C++, a search for "fixed atoms"

Re: [Rdkit-discuss] mmFF minimization in context of two ligands/binding pocket

Hi Steven, No. 1) is exactly what I'm doing to preform rigid protein minimization of ligands. I use ff.AddFixedPoint() to fix all protein atoms (you could omit the desired side chains). For better performance I also use following params: ff = AllChem.MMFFGetMoleculeForceField(comp, ff_mp,

[Rdkit-discuss] mmFF minimization in context of two ligands/binding pocket

Hi, Is it possible to do a minimization in mmFF in context of two small-molecules or a single small molecule and sidechains from a binding pocket? From what I gather, I have two options: 1) Make a single RWMol object with the ligand and all residues from the binding pocket, then run mmFF on the

[Rdkit-discuss] blog post: Thinking about an RDKit support model

Dear all, Some of you may not have seen this on LinkedIn or Twitter, so I'm posting here too: https://medium.com/@greg.landrum_t5/thinking-about-an-rdkit-support-model-782cfeb576a3#.n4e5u2tjx Note: I posted that yesterday! it's not a 1st of April joke! :-) I don't necessarily want to spam this