Atomdefinition for charged and uncharged Atoms

Ralph Gauges Ralph.Gauges@EMBL-Heidelberg.de
Mon, 09 Nov 1998 10:01:42 +0100


Hi,

I am trying to set up a system which includes hem groups and I have
encountered the following problem. The mmtk package does not include an
atom definition of Fe.  So I would like to try to define it myself, but
I have some questions beforehand.  First, do the methods in the mmtk
module make a difference between charged and uncharged atoms?  I assume
yes, because otherwise a lot would not make any sense.  But if yes, then

where do the methods get the information about charged residues
from(like van-der-Waals radii)?  Do I have to have a seperate set of
definition files for all the charged atoms, like one file for Fe, one
File for Fe2+ etc?  What would a definition file for a charged atom look

like?
I guess, somebody else must have had a similar problem before and
probably posted it.  Is there a way to read old posts from this mailing
list?


Thanks a lot

                            Ralph