VMD-L Mailing List

From: Snehasis Chatterjee (snehasis.chatterjee18_at_gmail.com)
Date: Tue Oct 15 2019 - 15:38:28 CDT

Dear VMD users,

I am trying to calculate inner volume of a Micelle using recently developed*
"measure* *volinterior" *tool. I am using new version of VMD (1.9.4). I
read the main paper (*Perilla **et. al.*, *Journal of Chemical Information
and Modeling*, 2019) and I am using these commands for calculating the
inner volume mentioned in the paper. Please see the commands below.

set molid [mol new snap_200ns_center.pdb waitfor all]
set RadiusScale 1.2
set Isovalue 0.9
set GridSpacing 2
set n 64

set sel [atomselect top "protein and not hydrogen"]
*set Nvoxels [measure volinterior $sel -res [expr $RadiusScale / 0.2]
-isovalue $Isovalue -spacing $GridSpacing -nrays $n -mol $molid]*
*set VoxelsIn [lindex $Nvoxels 2]*

I also used different parameters based on the paper (Table 1). But, the
inner volume of micelle is always zero.

Any kind of advice/ suggestions will be deeply appreciated.

Thanks in advance,
Snehasis Chatterjee