[gmx-users] source of opls Mg2+ parameters?

chris.neale at utoronto.ca chris.neale at utoronto.ca
Thu Nov 3 15:18:41 CET 2011

Thank you Tom!

Aqvist_A12 = sqrt(gromacs_C12*10^12/4.184)
Aqvist_A6 = sqrt(gromacs_C6*10^6/4.184)

(equation verified based on the SPC water oxygen parameters, also  
listed in Aqvist).

This reference (Aqvist, J (1990) J. Phys. Chem., 94 (21), pp  
8021?8024) should probably be noted somewhere in ions.itp or in  
ffoplsaa.itp. That might help stop these non-opls parameters from  
being cited as opls parameters.


-- original message --

Hi Chris,

If I remember correctly the magnesium ion parameters are the Aquvist
parameters (http://pubs.acs.org/doi/abs/10.1021/j100384a009).



chris.neale at utoronto.ca wrote:

[Hide Quoted Text]
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Mg2+ parameters from an unpublished source: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.

More information about the gromacs.org_gmx-users mailing list