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" in Code/ForceField/MMFF/testMMFFForceField.cpp will point you to
an example how to set fixed atoms.
To minimize a ligand in the context of a protein pocket I would combine
the ligand and the relevant residues in a ROMol, set the desired
contraints and then minimize. Please do not hesitate to get back to me
if you run into trouble.
Cheers,
p.
On 01/04/2016 16:29, Steven Combs wrote:
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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