[gmx-users] source of opls Mg2+ parameters?
t.piggot at soton.ac.uk
Thu Nov 3 11:19:42 CET 2011
If I remember correctly the magnesium ion parameters are the Aquvist
chris.neale at utoronto.ca wrote:
> Dear users:
> does anybody know where the OPLS magnesium parameters are from? As far
> as I can tell, they are not in Jorgensen 1996 or Kaminski 2001, In
> spite of the fact that many simulation studies reference these papers
> for their magnesium opls parameters.
> In fact, I do not think that the opls mg2+ parameters in ions.itp are
> taken from any of the references listed in ffoplsaa.itp. I checked the
> following references with searches for magnesium, mg2+, and a general
> visual scan:
> ; W. L. Jorgensen, D. S. Maxwell, and J. Tirado-Rives,
> ; J. Am. Chem. Soc. 118, 11225-11236 (1996).
> ; W. L. Jorgensen and N. A. McDonald, Theochem 424, 145-155 (1998).
> ; W. L. Jorgensen and N. A. McDonald, J. Phys. Chem. B 102, 8049-8059 (1998).
> ; R. C. Rizzo and W. L. Jorgensen, J. Am. Chem. Soc. 121, 4827-4836 (1999).
> ; M. L. Price, D. Ostrovsky, and W. L. Jorgensen, J. Comp. Chem. (2001).
> ; E. K. Watkins and W. L. Jorgensen, J. Phys. Chem. A 105, 4118-4125 (2001).
> ; G. A. Kaminski, R.A. Friesner, J.Tirado-Rives and W.L. Jorgensen, J.
> Phys. Chem. B 105, 6474 (2001).
> From a web search, the TINKER program indicates that it uses OPLS
> Mg2+ parameters from an unpublished source:
> "OPLS All-Atom Parameters for Organic Molecules, Ions, Peptides &
> Nucleic Acids, July 2008" as provided by W. L. Jorgensen, Yale
> University during June 2009. These parameters are taken from those
> distributed with BOSS Version 4.8.
> (above quote from http://dasher.wustl.edu/ffe/distribution/params/oplsaa.prm )
> although those tinker parameters (sigma=0.1450 and epsilon=3.9600) do
> not match the values for opls in the gromacs ions.itp (sigma=0.164447
> and epsilon=3.66118). I did not check out BOSS directly (it costs
> money), but I did look at the manual on the Jorgensen web page,
> although that manual does not contain Mg2+ parameters.
> I also checked the gromos magnesium parameters that are distributed
> with gromacs and verified that these c6/c12 values do not match the
> sigma/epsilon opls values after a conversion with g_sigeps.
> Thank you very much for your time and assistance,
Dr Thomas Piggot
University of Southampton, UK.
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