VMD-L Mailing List
From: zoran (zmatovic_at_kg.ac.rs)
Date: Sat Dec 13 2014 - 16:04:25 CST
Please have a look my post from December 14th. I clearly stated my problems there so if You did take a time to read it I cannot understand your words: “A blanket statement that it doesn't work isn't helpful”. I am ready to send the same files already sent to Christopher.
A sentence “ FFTK DOES work for many atom types, including new chemistries not found in released force fields” is just VERBAL support to this code without any reason (as I wrote that fftk is a good param. tool but not for neW atom types) and any further advice in this respect.
What’s up to me transition metals are not only an obstruction to finalize parametrization as I think reasonably that there is a bug with new atom types. So if You think that I am wrong please would You support it by examples (personal or papers published).
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.
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