VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 19 2012 - 20:59:32 CDT

Hi,
  Which precise version of NAMD were you running, and can you provide us
with the files that triggered the problem? It sounds like the NAMD process
died, which may be a bug with the new GBIS feature that may have
already been fixed very recently. To make sure, we need to know more details.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Apr 20, 2012 at 06:42:53AM +0530, amin_at_imtech.res.in wrote:
> Dear all,
> I ran a short GBIS simulation of a protein ligand complex as described
> in the Linear Interaction Energy Tutorial by John E.Kerrigan. Everything
> went fine but I am not able to get the VDW and Elec energies using NAMD
> energy plugin. I have tried for both just the ligand and the complex but I
> keep getting "Error:child killed:segmentation violation". The details of
> the error are
>
> child killed: segmentation violation
> child killed: segmentation violation
> while executing
> "exec $namdcmd ${jobname}-temp.namd > ${jobname}-temp.log"
> (procedure "namdrun" line 56)
> invoked from within
> "namdrun"
> (procedure "namdmain" line 76)
> 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 22)
> invoked from within
> "tk::ButtonUp .namdenergy.gobutton"
> (command bound to event)
>
> Can someone please help with this.
> Thanks.
>
>
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>
>
> ______________________________________________________________________
> ?????????????????????????????? ???????????????????????????????????? ????????????????????? (??????????????????????????? ???????????????????????? ???????????????????????? ???????????????)
> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
> ?????????????????? 39 ???, ???????????????????????? / Sector 39-A, Chandigarh
> ????????? ?????????/PIN CODE :160036
> ??????????????????/EPABX :0172 6665 201-202 

-- 
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