Dear Jim,
I have indeed written some preliminary code to:
1) Implement MMFF94/MMFF94s into OpenMM
2) Integrate OpenMM within the RDKit
Even though it needs polishing and adding unit tests, this code is
functional and usable.
I will make sure that it builds and integrates correctly with the
current version of OpenMM and RDKit and notify the mailing list as soon
as this is done.
Cheers,
p.
On 04/13/19 19:13, James T. Metz via Rdkit-discuss wrote:
RDkit Discussion Group,
I am aware of RDkit scripts that use the MMFF force field to
minimize small
molecules. Has anyone written RDkit code to perform molecular
dynamics (MD)
of small molecules or protein-ligand complexes using only RDkit and
existing
RDkit force fields. I am aware of a number of other programs to
perform MD, but
I am specifically interested in RDkit/Python only codes at present
i.e., no other
dependencies. If anyone has any code, even if preliminary, that
calculates the
potential energies, forces, velocities, accelerations, etc to
propagate the motions
of the atoms, and is willing to share that would be much appreciated.
Regards,
Jim Metz
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