Hi Dave,
we are preparing some updated side chain dihedrals and hopefullywill have
these and some modified backbone parameters by the nd of summer. I'd be
happy to share them as soon as we're done and would like to try out your
changes too. I think having all of our updates in a single paper and ff
library would make sense.
carlos
On Wed, Jun 17, 2009 at 1:47 PM, David A. Case <case.biomaps.rutgers.edu>wrote:
> 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
>
>
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Received on Mon Jul 06 2009 - 09:56:07 PDT
