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, nonBondedThresh=10.,
ignoreInterfragInteractions=False)
where comp is complex Mol, ff_mp are force-field molecular properties.
PS. There is no C++ API to my knowledge, although Greg/Paolo might have
something in his undocumented wizard hat ;)
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2016-04-01 17:29 GMT+02:00 Steven Combs <steven.com...@gmail.com>:
> 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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