VMD-L Mailing List

From: zoran (zmatovic_at_kg.ac.rs)
Date: Thu Dec 11 2014 - 03:30:25 CST

Dear Christopher,
Thanks for the e-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 the bug named Zoran-FFTK crash this for me so much wanted finalization.
I send You (and if there is people ready to help I’ll send files to them also) all the files I got it till now.

I desperately needs a help.

With my really best regards

Zoran

Dr Zoran D. Matović, professor of chemistry
Head of the Department of Chemistry
Department of Chemistry
Faculty of Science
University of Kragujevac
34000 Kragujevac
Serbia

Tel/Fax + 381 34 336 223 / 381 34 335 040

web-site:
http://www.pmf.kg.ac.rs/~zmatovic/index.htm

Lab for Supercomputing:
http://kraguj.pmf.kg.ac.rs/index.htm