[gmx-users] bug in ffoplsaanb.itp?
dmobley at gmail.com
Fri Mar 30 23:30:14 CEST 2007
Erik and all,
> No, I don't think so, or at least it's not our typo :-)
> It is quite common that ions end up with strange radii when you
> parametrize for free energy of solvation, and in addition those
> parameters are somewhat old (1984). Here's the extract from Bill
> Jorgensens file that we translated them automatically from:
> 400 09 F- -1.0 2.73295 0.72000 F- JACS 106, 903 (1984)
> 401 17 ?? -1.0 4.41724 0.11779 Cl- JACS 106, 903 (1984)
> 402 35 ?? -1.0 4.62376 0.09000 Br- JACS 107, 7793(1985)
> 404 03 Li 1.0 1.25992 6.25000 Li+ JACS 106, 903 (1984)
> 405 11 Na 1.0 1.89744 1.60714 Na+ JACS 106, 903 (1984)
OK, that is weird. If I plot the Cl potential energies from AMBER and
OPLS, they are almost identical. But if I plot F from OPLS versus F
from AMBER, the well is roughly, well, 10x as deep in OPLS as AMBER...
I guess you're off the hook in terms of it being your typo... But I'm
still not convinced it's right. Ugh. My understanding is that the LJ
parameters from AMBER and OPLS have roughly similar origins, so it
doesn't make a lot of sense to me to just say that AMBER is wrong --
especially when Cl and the other ion parameters are pretty consistent.
I suppose I will have to dig into the literature. Anyway, thanks for
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