VMD-L Mailing List
From: Jana, Suvamay (sja236_at_g.uky.edu)
Date: Mon Oct 28 2013 - 13:02:40 CDT
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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
- Next message: Himanshu Joshi: "Hydrogen Bond Calculation in VMD for DNA in VMD"
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- Reply: John Stone: "Re: namdenergy pugin for interaction energy"
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