VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Aug 28 2015 - 01:33:32 CDT

Hi,
  I'm assuming this is likely a memory capacity issue of
some kind. How large were your input files?

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Aug 23, 2015 at 07:29:08PM +0430, Atila Petrosian wrote:
> Dear VMD users,
>
> I am embedding proteins in membrane using
> http://www.ks.uiuc.edu/Research/vmd/plugins/membrane/
>
> At first, I made following files which are needed for combine.tcl file:
>
> readpsf membrane.psf
> coordpdb membrane.pdb
> readpsf protein.psf
> coordpdb protein_aligned.pdb
>
> When I used: vmd -dispdev text < combine.tcl | tee combine.log =>
>
> couldn't execute "tee": no such file or directory
>
> When I used: vmd -dispdev text -eofexit < combine.tcl =>
>
> VMD not responding
>
> When I used: vmd -dispdev text -e combine.tcl
>
> winvmd has stopped working, but I had following in VMD TkConsole:
>
> Info) VMD for WIN32, version 1.9.1 (February 1, 2012)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> Info) Please include this reference in published work using VMD:
> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
> Info) -------------------------------------------------------------
> Info) Multithreading available, 4 CPUs detected.
> Info) Free system memory: 958MB (46%)
> Info) No joysticks found. Joystick interface disabled.
> Info) Dynamically loaded 69 plugins in directory:
> Info) C:/Program Files/University of Illinois/VMD/plugins/WIN32/molfile
> 1.6
> psfgen) reading topology file top_all27_prot_lipid.inp
>
> psfgen) >>>>>> Combined CHARMM All-Hydrogen Topology File for <<<<<<<<<
> psfgen) >>>>>>>>> CHARMM22 Proteins and CHARMM27 Lipids <<<<<<<<<<
> psfgen) from
> psfgen) >>>>>>>>CHARMM22 All-Hydrogen Topology File for Proteins <<<<<<
> psfgen) >>>>>>>>>>>>>>>>>>>>> August 1999 <<<<<<<<<<<<<<<<<<<<<<<<<<<<<
> psfgen) >>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<
> psfgen) >>>>>> 410-706-7442 or email: alex,mmiris.ab.umd.edu <<<<<<<<<
> psfgen) and
> psfgen) \\\\\\\ CHARMM27 All-Hydrogen Lipid Topology File ///////
> psfgen) \\\\\\\\\\\\\\\\\\ Developmental /////////////////////////
> psfgen) Alexander D. MacKerell Jr.
> psfgen) August 1999
> psfgen) All comments to ADM jr. email: alex,mmiris.ab.umd.edu
> psfgen) telephone: 410-706-7442
> psfgen)
> psfgen) Created by CHARMM version 27 1
> psfgen) clearing structure, preserving topology and aliases
> psfgen) reading structure from psf file membrane.psf
> child killed: segmentation violation
>
> What is the reason of "child killed: segmentation violation"?
>
> Any help will highly appreciated. 

-- 
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/