[MMTK] Amino acid definition files

Berit Hinnemann Berit.Hinnemann@fysik.dtu.dk
Fri, 16 Nov 2001 15:22:03 +0100

Hi Konrad,

when amber charges are defined in the amino acid definition file, then I
cannot override them by assigning an attribute "amber_charge" to atoms,
after they have been read in from the PDB file. Is this right, or is
there a way to override them, which I have missed?

Did you design it like that for speed reasons, because looking in the
database is faster and most of the time the default charges are wanted
anyway? It is not a problem, as I use user-defined amino acid definition
files without amber charge definitions, I am just interested in the
reasons for the design.

Thanks a lot,
Berit Hinnemann
Center for Atomic-Scale Materials Physics (CAMP)
Dept. of Physics, Technical University of Denmark
Building 307, DK-2800 Lyngby, Denmark 
Phone: +45 4525 3209, Fax: +45 4593 2399