VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Oct 31 2013 - 10:03:26 CDT

Hi,
  The error messages you've gotten seem to indicate that either one of
your atom selections might be inappropriate, or that the mass field of
your structure is uninitialized. Have you re-checked your atom selections
to make sure that they are correct for all of the trajectory frames you
intend to analyze?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Oct 28, 2013 at 02:02:40PM -0400, Jana, Suvamay wrote:
> 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 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/