On Wed, Nov 23, 2011 at 11:59 PM, Raik Grünberg <raik.gruenberg.gmail.com>wrote:
> Thanks! Switching to ff10 solved it.
>
> I run into another issue with a Na+ ion because the ff10 leaprc file
> includes ions08.lib but doesn't fully parametrize the ions defined
> there. Very confusing -- because ions are correctly recognized but the
> topology can then anyway not be saved. A water-model-specific mod
> file needs to be loaded to finish the job. I see that this is supposed
> to be feature rather than bug but then it would be much less
> troublesome to either have a complete parametrization (by default for
> TIP3) or have no ion definitions included at all.
>
Different water models are appropriate for different simulations, so
there's no water model we can just "assume" people will want. If we did,
then we would mask errors for users that want to use, for example, TIP4P or
TIP4Pew or something like that.
Perhaps we could have a separate leaprc for different water models, so we'd
have something like "source leaprc.ff10; source leaprc.tip3p" which would
load the parameters and libraries for the water models as well as the ion
parameters, I'm not sure which would be easier.
Furthermore, there's nothing stopping users from creating their own leaprc
file if that's behavior that they want ;).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Nov 23 2011 - 22:00:03 PST
