VMD-L Mailing List

From: zoran (zmatovic_at_kg.ac.rs)
Date: Sat Dec 13 2014 - 06:50:49 CST

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