After defining atom types and partial
charges, I am trying to add hydrogens to a
ligand. On using the "add H and build", i only get
some hydrogens.
The hybridization is key here - e.g. in leaprc:
# load atom type hybridizations
#
addAtomTypes {
{ "H" "H" "sp3" }
{ "HO" "H" "sp3" }
...
Also, the bond orders are
incorrect, with double bonds not appearing. Can
anyone advise me?
At this point, the bond orders only apply to "add H and build"
and the minimization of atoms without types or with types lacking
parameters. They must be set by hand, by clicking on the bond.
Bond orders will probably receive more attention when automatic
parameter assignment is "ready for prime-time."
Bill Ross
Received on Fri Jun 09 2000 - 11:28:28 PDT
