We are currently trying to modify
AMBER prmtop files for our own pseudoatom model.
everything is quite clear except the 'excluded atoms'.
we would be grateful if someone could tell us
what this is all about. i.e. what are excluded atoms
for "atom i" (quoted from the AMBER docomentation) ?
N-B interactions are not calculated for atoms associated by
bonds, angles or dihedrals, so these atoms are explicitly
excluded; the list is cumulative, i.e. each atom only lists
ones that follow it.
Search for "Build the excluded atom list" in leap's unitio.c
to see some code.
Bill Ross
Received on Wed Sep 27 2000 - 09:06:57 PDT
