From: 本村肇 (h-motomura_at_bioreg.kyushu-u.ac.jp)
Date: Mon Nov 20 2017 - 21:47:25 CST

I tried 6pti.pdb tutorial, however an error occurred. It was "invalid command name “psfgen”".

Its URL is following :
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node17.html

My setup file is following :
# File: bpti_example.tcl
# Requirements: topology file top_all22_prot.inp in directory toppar
# PDB file 6PTI.pdb in current directory
# Create working directory; remove old output files
mkdir -p output
rm -f output/6PTI_protein.pdb output/6PTI_water.pdb
# (1) Split input PDB file into segments}
grep -v "^HETATM" 6PTI.pdb > output/6PTI_protein.pdb
grep "HOH" 6PTI.pdb > output/6PTI_water.pdb
# (2) Embed the psfgen commands in this script
#added by motomura
#package require psfgen
psfgen << ENDMOL

An error code is following :
bash-3.2$ vmd -dispdev text < 1set.tcl | tee 1set.out;
Info) VMD for MACOSXX86, version 1.9.4a8 (August 30, 2017)
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) Dynamically loaded 2 plugins in directory:
Info) /Applications/VMD_1.9.4.app/Contents/vmd/plugins/MACOSXX86/molfile
invalid command name "psfgen"
Info) VMD for MACOSXX86, version 1.9.4a8 (August 30, 2017)
Info) Exiting normally.
bash-3.2$ vmd -dispdev text < 1set.tcl | tee 1set.out;
Info) VMD for MACOSXX86, version 1.9.4a8 (August 30, 2017)
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) Dynamically loaded 2 plugins in directory:
Info) /Applications/VMD_1.9.4.app/Contents/vmd/plugins/MACOSXX86/molfile
1.7
invalid command name "psfgen"
Info) VMD for MACOSXX86, version 1.9.4a8 (August 30, 2017)
Info) Exiting normally.