VMD-L Mailing List

From: 本村肇 (h-motomura_at_bioreg.kyushu-u.ac.jp)
Date: Mon Nov 20 2017 - 23:34:40 CST

Thank you for your reply.
"package require psfgen” is not in the tutorial, so I added it.
However an error was occurred.

> 2017/11/21 14:22、Ashar Malik <asharjm_at_gmail.com>のメール:
>
> The following line is commented.
>
> #package require psfgen
>
> Uncomment it.
>
> On Nov 21, 2017 17:05, <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.
>