VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Fri Oct 02 2015 - 01:03:27 CDT

Hi James:
I am carrying out repeated opt-freq (just to be sure to have a clean log
file) of the metal cluster at B3LYP/6-31G*. Therefore, if I understand, the
Gaussian log file should be handled by ffTK at its present release. If not,
I would be grateful for your additional code. I'll let you know.

A cluster with two bridged Fe(II) is not the easiest way to approach this
problem with ffTK. Just devising Fe atom types for Fe at the center of (a)
trigonal bi-pyramid and (b) square bi-pyramid Fe(II), with equatorial O
atoms and axial N, O atoms is - for me - no trivial task. If you have any
suggestion about model atom types from which to begin, it would be great
help.

thanks

francesco pietra

On Thu, Oct 1, 2015 at 11:38 PM, JC Gumbart <gumbart_at_ks.uiuc.edu> wrote:

> 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 (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
>
>
>