From: Jana, Suvamay (sja236_at_g.uky.edu)
Date: Mon Oct 28 2013 - 13:02:40 CDT

Hi,

I am trying to use namdenergy plugin of vmd-1.9.1 to compute non-bonded
interaction energy in between my protein-ligand system. I initially built
my system in charmm 36 and converted the charmm .psf file in namd xplor
format and ran namd md simulation.
I performed recenter and orient my namd output .dcd files in charmm and
obtained a new .dcd file which I loaded in vmd.
And while calculating interaction energy Its giving me the following error.

measure center: bad weight sum, would cause divide by zero
measure center: bad weight sum, would cause divide by zero
    while executing
"measure center $sel1 weight mass"
    (procedure "namdconf" line 307)
    invoked from within
"namdconf"
    (procedure "namdmain" line 71)
    invoked from within
"namdmain"
    (in namespace inscope "::namdEnergy" script line 19)
    invoked from within
"::namespace inscope ::namdEnergy {
      mol top $currentMol
      variable sel1
      variable sel2
      variable nsel
      set energy ""
      set..."
    invoked from within
".namdenergy.gobutton invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 23)
    invoked from within
"tk::ButtonUp .namdenergy.gobutton"
    (command bound to event)

Can anybody please help me by telling what may be the possible reason
behind this?

With Regards,

Suvamay Jana