[gmx-users] bug in ffoplsaanb.itp?
lindahl at cbr.su.se
Fri Mar 30 22:59:14 CEST 2007
On Mar 30, 2007, at 10:12 PM, David Mobley wrote:
> I'm looking at the epsilon value in ffoplsaanb.itp (i.e. from CVS of
> 3.3.1) for opls_400, F-. It's lilsted as 3.01248e00. This is roughly a
> factor of 10 larger than many of the other anions (i.e. Cl) and also
> roughly a factor of 10 larger than the AMBER96 value (in the same
> units) for F-: 2.552e-01.
> I assume that this is a typo in the opls file, and the correct value
> should be 3.01248e-01?
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)
You can probably figure out the columns yourself, but OPLS type 400
has sigma=2.73295 and epsilon=0.72 (in angstroms and kcal units).
I'll be happy to send you the entire file offline if you're interested.
PS: The constraint patch should be in CVS now, and the lambda-stuff
is getting there!
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