Hi everyone:
I'm attaching a paper sent me by Edyta Malolepsza, pointing out that the
Amber force fields are not invariant to permutations among equivalent atoms
in a variety of cases. (For example, if you swap OD1 and OD2 in asp, you
might get a slightly different energy.) There is also a proposed fix.
I don't think we can just patch the prep files at this point, since that
would upset backwards compatibility. But I am thinking that we should put
these changes into the next versions of all our force fields, since that
would just represent one improvement (among others) of the new ff's over the
old ones.
There remains the question of how to implement this; ideally, tleap and sleap
would be modified, somehow(?) knowing when to use the new rules and when to
use the old ones. Alternatively, we could post-process the prmtop files, as
suggested in the paper.
Comments are welcome, both from developers and from people in the Amber FF
consortium.
As an aside, I'm eager to hear about progress in efforts to release updated
force fields. I have some suggested changes for ff99SB and ff03 (involving
LJ 6-12 parameters on His, Lys and Arg sidechains) that I think are worth
testing. But I'm also aware that we don't want to put out force field
updates in a piecemeal fashion, and I'd be eager to collaborate.
..thx...dac
Received on Mon Jul 06 2009 - 09:55:47 PDT
