VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Nov 20 2017 - 23:22:31 CST

The following line is commented.

#package require psfgen

Uncomment it.

On Nov 21, 2017 17:05, "本村肇" <h-motomura_at_bioreg.kyushu-u.ac.jp> wrote:

> 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.
>
>