VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Sat Dec 13 2014 - 13:54:38 CST

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:
> Christopher
> 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
> Zoran