Hi, I'm trying to do some surface area calculations on MARTINI models using APBS, which requires supplying vdw radii via a pqr file. Given how MARTINI treats LJ interactions (0.47 nm radius for all particle types), how do I calculate reasonable effective vdw radii? Obviously the PC headgroup (NC3) will have a larger vdw radius than the PE headgroup (NH3), and g_sas seems to account for this (reported ASA for -NC3 group is always higher than for -NH3 group) but I can't figure out how. Indeed, using "editconf -mead" to produce a pqr file from a MARTINI structure shows 2.35 A as the vdw radius for all lipid groups, which I fear will cause inaccurate calculations in APBS. Has anyone had this problem before?
Mike -- ==================================== Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison)
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