VMD-L Mailing List
From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Apr 19 2012 - 20:59:32 CDT
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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.
>
>
> ______________________________________________________________________
> ?????????????????????????????? ???????????????????????????????????? ????????????????????? (??????????????????????????? ???????????????????????? ???????????????????????? ???????????????)
> Institute of Microbial Technology (A CONSTITUENT ESTABLISHMENT OF CSIR)
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> ????????? ?????????/PIN CODE :160036
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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
-- NIH Resource 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/ Fax: 217-244-6078
- Next message: Donovan B.T.: "AutoPSF"
- Previous message: Andrés Morales: "Re: Thickness of bilayer script"
- In reply to: amin_at_imtech.res.in: "segmentation fault with NAMDenergy"
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