VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Sep 27 2015 - 13:20:28 CDT

Hello:

There was some discussion about parameterizing transition metal proteins at
the onset of ffTK, in February 2012.

I have lost details on how ffTK has been further developed, however I came
across a recent statement that the QM part of ffTK was taken from Paratool.
As the latter was originally applied to parameterize a non-heme iron
protein active center (in a way that was focused on deriving bond, angle
etc forces, not atom partial charges, just to have a "dirty"
parameterization that keeps the structure of the active center in order
during MD

 my question is:

Has anyone verified whether the QM part of current ffTK works with a
Gaussian log file from a DFT calculation with models of transition metal
centers of proteins? My aim is "merely" to have such forces rapidly
extracted from the QM matrix (the way that MCPB does that in Amber world
for Zn(II) complexes), so that many variations of the coordination
situation around the transition metal can be investigated.
Which is probably the upper limit for MD dealing with transition metal
proteins. However, such proteins make a large fraction of life.

thanks
francesco pietra