VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Thu Oct 01 2015 - 16:38:01 CDT

Hi Francesco,

Dealing with transition metals is a huge problem for both QM and MD. I recognized that the bond/angle part of FFTK (because of its reliance on the QMTool plugin) can’t handle any DFT methods other than B3LYP. We’ve recently used BP86, so I changed the source code to add the scaling factor for this method. All force constants read from the hessian have to get scaled slightly, with HF being the biggest (about (0.9)^2) and the DFT methods being much lower (BP86 is (0.99)^2). If you want, I can share the source-code with you off-list; it’s just a few small changes.

See this paper for more discussion: http://pubs.acs.org/doi/abs/10.1021/jp960976r <http://pubs.acs.org/doi/abs/10.1021/jp960976r> (wow, it’s been cited 6000 times!)

I’m really glad you asked this question, as I hadn’t looked at that part of the code for a very long time!

Best,
JC

> On Sep 27, 2015, at 2:20 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>
> 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