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 combine molecule. The steps would look
like this
-use combineMols() for all residues
-use mmFF on the complex
2) Use a hacked version of MCS from here:
http://rdkit.blogspot.com/2013/12/using-allchemconstrainedembed.html
Is there a better way of doing this? I am using the C++ api.
Steven Combs
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