VMD-L Mailing List

From: mish (smncbr_at_gmail.com)
Date: Tue Mar 17 2015 - 11:10:28 CDT

Dear all,

Is there somehow possible in VMD to calculate volume of the 3D space
sampled by a ligand during the simulation in protein-ligand complex. I
tried using PortoBiocomp VolAra plug-in but there seems to be some issues.
I check Volume calculation and do dynamic analyses from 0 to 10 with Step
1. In Global selection window, I select my ligand (resid 260 261). As soon
I start calculation, it asks to save a .srfv file. Then it starts
calculation and then it pop-up and window "Application Error" with Error:
no such table: frame_0 with following detail.
no such table: frame_0
no such table: frame_0
    while executing
"$VolArea::namedb eval "SELECT sasa FROM frame_$i WHERE resname=:name""
    (procedure "VolArea::calcall" line 10)
    invoked from within
"VolArea::calcall"
    (procedure "VolArea::RunButton" line 111)
    invoked from within
"VolArea::RunButton"
    invoked from within
".volarea.nb1.fp.rru.b1 invoke "
    invoked from within
".volarea.nb1.fp.rru.b1 instate {pressed !disabled} {
.volarea.nb1.fp.rru.b1 state !pressed; .volarea.nb1.fp.rru.b1 invoke } "
    (command bound to event)

I cant understand what is going wring. Is there some way to calculate
volume of the total ensemble of ligands from each frame. Moreover, using
VolMap tool I can save densities of all the frames combined using "max" in
file. If there is a way reading this "volmap_out.dx" file and calculation
volume of this in vmd, it should do what I am willing to do. I would
appreciate any help in make it working any of the two ways.

Best,
Mish