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"
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,
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
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