VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Nov 20 2017 - 23:47:19 CST

On Mon, Nov 20, 2017 at 10:47 PM, 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;
>

​what you are doing here makes no sense.
it is decidedly different from the tutorial you reference, which
*expli​citly* states that it uses the standalone "psfgen" command which is
bundled with NAMD, while you are trying to feed the script to VMD, which is
not the same.

in addition, the script you have is a bourne shell script and not a Tcl
script.

if you want to follow the tutorial, you have to *correctly* follow it, and
not make up stuff that is different and thus guaranteed to fail.

axel.

> 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.
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.