The paper has finally been accepted for publication (1), so I am posting these NBFIX parameters which have been validated with the anionic lipids DMPG and POPS, and also developed wrt. to neutral phospholipids. We have also been using them in our own lab during the validation of parameters for other anionic lipids, such as cardiolipins and phosphoinositols (manuscripts in preparation).

The NBFIX values below assume the use of the more recent Na+ L-J parameters of Noskov and Roux (2) and NBFIX for the Na+:Cl- pair (3), which are both now included with the C36 parameter bundle. All of the values listed below are new, including the SOD:OCL term, which was very recently revised (Rmin was initially 3.19) during final validation. While developed and tested for lipid surfaces where the local concentration of anionic groups is very high, it is likely these values are more broadly applicable to other CHARMM biopolymer force fields.

Code:
NBFIX
!               Emin        Rmin
!            (kcal/mol)     (A)

! J. Phys. Chem. B 2013, in press
SOD    OCL      -0.07502    3.23    ! carboxylate =O ; yun luo, osmotic P
SOD    OBL      -0.07502    3.13    ! ester =O ; yun luo, POPC optim.
SOD    O2L      -0.07502    3.16    ! phosphate =O ; yun luo, POPC optim.


(1) Simulations of Anionic Lipid Membranes: Development of Interaction-Specific Ion Parameters and Validation using NMR Data. Venable, R.M.; Luo, Y,; Gawrisch, K.; Roux, B.; Pastor, R.W. J. Phys. Chem. B 2013, 117 (35), pp 1018310192. DOI: 10.1021/jp401512z

(2) Noskov, S. Y.; Roux, B. Journal of Molecular Biology 2008, 377, 804-18.

(3) Luo, Y.; Roux, B. Physical Chemistry Letters 2010, 1, 183-189.

Last edited by rmv; 09/17/13 10:04 PM. Reason: update citation

Rick Venable
computational chemist