On Tue, Jun 12, 2012, Kevin Parkes wrote:
> Digging deeper it looks as if my problem may be because there
> are van der Waals parameters for fluorine in the last section of
> parm99.dat (loaded by leaprc.ff99SB) but not in param10.dat (loaded by
> leaprc.ff12SB). Where should these parameters now be loaded from?
It looks like it was perhaps a mistake to remove the F, Cl, Br and I LJ
parameters from the bottom of parm10.dat. I think we (I?) was trying to avoid
conflicts to halide ions (but the ions have atom types with a "-" in their
names, so there aren't any conflicts.
You should be able to copy the relevent lines from parm99.dat to parm10.dat.
But be sure to read the papers that are cited, and think about whether things
make sense. These parameters probably make general sense, but have not been
extensively tested. You might want to compare to the fluorine parameters in
GAFF to see if there are any significant differences.
....thanks for the report....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jun 12 2012 - 08:00:03 PDT
