[gmx-users] surface area calculations for MARTINI

[Michael Daily]

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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