Hi,<br><br>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?<br>
<br>Mike<br clear="all"><br>-- <br><font><font size="2">====================================<br>
Michael D. Daily<br>
Postdoctoral research associate<br>
Pacific Northwest National Lab (PNNL)<br>
<a href="tel:509-375-4581" value="+15093754581" target="_blank">509-375-4581</a><br>
(formerly Qiang Cui group, University of Wisconsin-Madison)</font></font><br>