From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Sun Oct 04 2015 - 08:23:55 CDT

You might be able to hack it together by creating a “fake” log file that includes the information FFTK and qmtool are looking for. You’ll want to dig into the source code a little to figure this out.

Best,
JC

> On Oct 4, 2015, at 7:01 AM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
>
> Unexpectedly, unlike in the past, I am unable to reproduce (Gaussian DFT B3LYP opt or opt=tight in vacuo) the crystal structure of the di-Fe(II) cluster. One Fe comes out correctly with a square bipyramid octahedral coordination. The coordination around the other Fe, which should include a water molecule, is disrupted: instead of a trigonal bipyramid coordination including water, the water molecule becomes H-bonded to a carboxylate and Fe is left in a awkward situation. That is of no interest to the audience. What may be of interest, is that I do not remember whether I used before an implicit environment for the quantum mechanical calculations. Otherwise, reproducing the crystal structure with calculations in vacuo should be viewed as a miracle for this complex cluster. A miracle that was not repeated in these days.
>
> Unfortunately, not all from previous calculations was saved (it was a couple of years ago, abandoned as I was unable to extract the force constants). The pdb, obtained at those time with newzmat, shows that the crystal structure was reproduced correctly. What else I still have is a .fchk file reporting the freq analysis only, and the related Hessian matrix that I extracted from the .chk file. Can these be submitted to ffTK or the complete Gaussian log file is needed?
>
> Thanks for a comment on in vacuo vs implicit solvent calculations and, of course, about the ffTK requirements.
>
> francesco
>
> On Sat, Oct 3, 2015 at 10:55 PM, JC Gumbart <gumbart_at_ks.uiuc.edu <mailto:gumbart_at_ks.uiuc.edu>> wrote:
> You are fine then! qmtool already had the scaling factor for B3LYP frequencies built in.
>
> We are dealing with exactly the same issues with cobalamins with a Co(I), (II), or (III) at the center. But if it’s fully bonded, then what atom type you use is irrelevant. Just create a new one and then calculate all the bonded terms from scratch. We are struggling because we are trying to come up with rational LJ parameters for a Co atom that is not fully bonded.
>
> Best,
> JC
>
>
>> On Oct 2, 2015, at 2:03 AM, Francesco Pietra <chiendarret_at_gmail.com <mailto:chiendarret_at_gmail.com>> wrote:
>>
>> 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 <mailto: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 <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 <mailto: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
>>
>>
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