[MMTK] Difference in number of Torsion parameters between MMTK and Leap

Mark Williamson Mark.Williamson at imperial.ac.uk
Thu May 3 13:25:20 UTC 2007


Konrad Hinsen wrote:
> I assume that "pk" is the force constant prefactor in the dihedral
> terms. In 20 of the terms listed by RDPARAM, it is zero. These terms are
> automatically discarded by MMTK. Both AMBER and MMTK thus have 32
> non-zero dihedral energy terms, impropers included.

Thank you Konrad for your careful analysis of this and the clear
explanation.

> one of them based on a criterion of alphabetical order of atom types
> plus atom indices if the atom types are the same. As far as I know, this
> detail is nowhere documented; one of the AMBER developers explained it
> to me when I asked the question many years ago. MMTK applies the same
> rule as AMBER, but the atom indexing in MMTK and AMBER are in general
> not the same.
> 
In a similar vein to this (and may be of use to you), this relates to a
recent question I asked on the amber mailing list:

http://amber.ch.ic.ac.uk/dev-archive/200704/0005.html
http://amber.ch.ic.ac.uk/dev-archive/200704/0006.html

Hence, I think the parm94.dat (amber_parm94) distributed with MMTK may
need to have these changes applied.

Thanks again,


Mark



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