From: zoran (
Date: Sun Dec 14 2014 - 10:20:00 CST

Now I wish to again point out the problem about fftk and optimization of bonding parameters what was original reason for me to place this post.

I have already send all the files to Chris and You. However no answer may be because of previous useless debate.
I really asked for Your help with respect to fftk.
Josh, If You are right Is there any possibility to have valid answer or opinion on my questions and a subject of this post? I have no doubts about accuracy of the charges, bonds, angles and dihedrals optimizing by the automatism of fftk even in case of my complex just tell me how?
I’ll repeat my original mail:
I still cannot move further with optimization of bonds and angles in FFTK.
This time I’ll try to formulate my problem in a clear manner:
  1.. First I have done all the things requested by fftk:
        a) I prepared PSF & PDB Files Using Molefacture without many troubles (I assigned type of different atoms using all36_cgenff topology)

        b) I went through BuildPar (obtained pdobap-int.par) and updated with vdw LJ parameters. As You can see I placed vdwLJ values for Pd(II) taking these from the most similar work.

        c) I went through Opt.Geometry fine (here is to mention that I replaced 6-31G with sdd bs because of Pd) ; Water Int. almost fine as fftk (or some interfaced plugin; maybe qmtool) wrote Gaussian input file with P (phosphorous) instead of Pd (palladium), so I had to correct it through all the files manually. Do You know why is that so?

        d) However after that Opt. Charges went fine so I succeeded to update psf file with charges.

        e)I calculated hessian without any trouble
        f) Now I have problem with Calc. Bonded. I put all the requested items into input (psf, opt, hess log and int-par files leaving AA Parameter files empty and determined path for namd2.exe. Then I’ve dialed with Parameters to optimize.

Here is the problem: When I push ‘'Guess” button the program wrote all the bonds but only four angles (no palladium within them). Anyway I started “Run Optimization” and fftk (better to say namd) stopped with the warnings that some angle parameters are not present (here I red from Tk_console_log – attached- that Qmtools again transformed my Palladium into P).

I added manually, step by step these angles after every warning with corresponding values of angles from optimized molecule and placed random force constants for these angles. At the end when no angles left more program started requesting torsions this time. Ehhh, that’s put the last drop into my glass.

So You see I‘ve done everything requested but somewhere must be a bug that crash this for me so much wanted finalization.”

Hi Zoran,
What specific problems have you encountered? I don't see what is special about metals that they should result in problems for the methodology of FFTK. A blanket statement that it doesn't work isn't helpful, because as written FFTK DOES work for many atomtypes, including new chemistries not found in released force fields.
-Josh Vermaas

On 12/13/2014 06:50 AM, zoran wrote:

  I think that You actually never run fftk with molecule holding a new atom type. Is this true?
  Somewhere fftk has a bug while trying to optimize bonds and angles of molecules with new atom types. And I also think that this has not any matter with metals as a constituent (it could be let we say Boron or Phosphorous atom in diff. surroundings).

  I suppose You have no time and will to dig into fftk to correct it.

  However it is fair to say to the people that FFTK is not supposed to work with molecules containing new atom types. This does not represent anything that would diminish the importance of FFTK as a powerful tool.

  I say this accounting that I have done all requested tasks (including addition of vdwLJ values) and stacked into bonds and angles. I do not see any fault from my side so above is most probably true.

  I am very sorry that scientists making force fields for macromolecules forget on transition metals (in general) and that TM make a substantial part of biological processes.

  With my best regards to all of you