From: Atila Petrosian (
Date: Sun Aug 23 2015 - 09:59:08 CDT

Dear VMD users,

I am embedding proteins in membrane using

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) Email questions and bug reports to
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
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, <<<<<<<<<
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,
psfgen) telephone: 410-706-7442
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.