On Thu, Apr 12, 2007, Mark Williamson wrote:
>
> Why is there this difference between the parm94.dat with amber8 and the
> "same" one distributed with amber9? Can anyone confirm this? I've had a
> quick scan through the bugfixes, but I cannot seem to find anything that
> refers this change.
The convention adopted by LEaP for impropers is the following: the "middle"
atom is atom #3; the remaining three atoms (1,2, and 4) should be in
alphabetical order by atom type.
Some of the entries in parm94.dat did not follow this convention, and were
updated to conform. It is possible that this could cause small changes in the
energies of particular conformers. If you see bigger changes, you might bring
that to our attention. As far as we know, the "intent" of the original force
field parameterization is best represented by the amber9 version of the file.
...hope this helps...dac
Received on Sun Apr 15 2007 - 06:07:31 PDT
