[MMTK] Reading in of AMBER related files

Mark Williamson Mark.Williamson at imperial.ac.uk
Tue Apr 3 17:52:08 UTC 2007


Dear List,

Can MMTK parse in a AMBER parm topology file 
(http://amber.scripps.edu/formats.html) and then say evaluate the energy 
of a structure in a corresponding AMBER coordinate file?

Looking at an example at 
http://dirac.cnrs-orleans.fr/mmtk_wiki/ExampleScripts/ShowEnergies

It seems the AMBER topology is inferred from the PDB file upon adding of 
the Object to the universe.
Where do the electrostatic charges come from?
How does MMTK deal with non-standard resides?

Also, in a given universe, is it possible to list every dihedral term 
(with their parameters) within the force field that the universe is 
using? I suspect due to the OO nature of MMTK this would be quite easy 
to do.

Thanks in advance,

Mark



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