From: Matthew Bick (bickm_at_mail.rockefeller.edu)
Date: Mon May 30 2011 - 12:32:29 CDT

Dear Community. I am new to both NAMD and VMD. I am working through
the NAMD tutorials at the moment, but my issue concerns VMD.

First, my computer specs. I am using a Powerbook G4, 1.67 MHz running
OS 10.5.8. I am using VMD 1.9, and NAMD 2.8b3 for MacOSX PPC.

I am having trouble during the first part of the NAMD tutorial, where
you create the psf file for ubiquitin. This is on page 11 of the
tutorial. I have triple checked that I made the ubq.pgn file correctly:

package require psfgen
topology top_all27_prot_lipid.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment U {pdb ubqp.pdb}
coordpdb ubqp.pdb U
guesscoord
writepdb ubq.pdb
write psf ubq.psf

When I type "vmd -dispdev text -e ubq.pgn" at the command line (I have
aliased vmd successfully), the pdb file is generated, but not the psf
file. I get the following error (I'll post the entire thing as I
don't know what exactly is important):

$ vmd -dispdev text -e ubq.pgn
Info) VMD for MACOSX, version 1.9 (March 14, 2011)
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, 1 CPU detected.
1.5.0
reading topology file top_all27_prot_lipid.inp

> CHARMM22 All-Hydrogen Topology File for Proteins and Lipids <<
>>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<
>>>>>>>>>>>>>>>>>>>>>> July 2004 <<<<<<<<<<<<<<<<<<<<<<<<<<
  All comments to ADM jr. via the CHARMM web site: www.charmm.org
                parameter set discussion forum

Created by CHARMM version 31 1
cross-term entries present in topology definitions
aliasing residue HIS to HSE
aliasing residue ILE atom CD1 to CD
building segment U
reading residues from pdb file ubqp.pdb
extracted 76 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-HN at beginning of segment.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping cross-term C-N-CA-C-N-CA-C-N at end of segment.
Info: skipping conformation CA-C-N-CA at end of segment.
Info: skipping conformation N-CA-C-O at end of segment.
Info: skipping conformation N-CA-C-N at end of segment.
U:1
U:76
Info: segment complete.
reading coordinates from pdb file ubqp.pdb for segment U
Warning: failed to set coordinate for atom O GLY:76 U
Warning: failed to set coordinate for atom OXT GLY:76 U
Info: guessing coordinates for 631 atoms (2 non-hydrogen)
Warning: poorly guessed coordinates for 8 atoms (2 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1 MET:1 U
Warning: poorly guessed coordinate for atom HT2 MET:1 U
Warning: poorly guessed coordinate for atom HT3 MET:1 U
Warning: poorly guessed coordinate for atom HG2 PRO:19 U
Warning: poorly guessed coordinate for atom HG2 PRO:37 U
Warning: poorly guessed coordinate for atom HG2 PRO:38 U
Warning: poorly guessed coordinate for atom OT1 GLY:76 U
Warning: poorly guessed coordinate for atom OT2 GLY:76 U
Info: writing pdb file ubq.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.
write: psf is not logged in on ubq.psf
child process exited abnormally
vmd >

If I launch VMD in text mode, using "/Applications/VMD\ 1.9.app/
Contents/vmd/vmd_MACOSX dispdev text -e ubq.pgn", I get the same
result (pdb file generated, but psf file not) with a slightly
different error message:

$ /Applications/VMD\ 1.9.app/Contents/vmd/vmd_MACOSX dispdev text -e
ubq.pgn
Info) VMD for MACOSX, version 1.9 (March 14, 2011)
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, 1 CPU detected.
Info) OpenGL renderer: ATI Radeon 9600 XT OpenGL Engine
Info) Features: STENCIL MTX NPOT PS GLSL(VF)
Info) GLSL rendering mode is NOT available.
Info) Textures: 2-D (2048x2048), 3-D (256x256x256), Multitexture (8)
Info) File loading in progress, please wait.
Warning) Unable to ascertain filetype from filename 'dispdev';
assuming pdb.
ERROR) Could not read file dispdev
ERROR) Loading of startup molecule files aborted.
1.5.0
reading topology file top_all27_prot_lipid.inp

> CHARMM22 All-Hydrogen Topology File for Proteins and Lipids <<
>>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<
>>>>>>>>>>>>>>>>>>>>>> July 2004 <<<<<<<<<<<<<<<<<<<<<<<<<<
  All comments to ADM jr. via the CHARMM web site: www.charmm.org
                parameter set discussion forum

Created by CHARMM version 31 1
cross-term entries present in topology definitions
aliasing residue HIS to HSE
aliasing residue ILE atom CD1 to CD
building segment U
reading residues from pdb file ubqp.pdb
extracted 76 residues from pdb file
Info: generating structure...
Info: skipping improper N-C-CA-HN at beginning of segment.
Info: skipping cross-term C-N-CA-C-N-CA-C-N at beginning of segment.
Info: skipping conformation C-N-CA-C at beginning of segment.
Info: skipping conformation C-CA-N-HN at beginning of segment.
Info: skipping bond C-N at end of segment.
Info: skipping improper C-CA-N-O at end of segment.
Info: skipping cross-term C-N-CA-C-N-CA-C-N at end of segment.
Info: skipping conformation CA-C-N-CA at end of segment.
Info: skipping conformation N-CA-C-O at end of segment.
Info: skipping conformation N-CA-C-N at end of segment.
U:1
U:76
Info: segment complete.
reading coordinates from pdb file ubqp.pdb for segment U
Warning: failed to set coordinate for atom O GLY:76 U
Warning: failed to set coordinate for atom OXT GLY:76 U
Info: guessing coordinates for 631 atoms (2 non-hydrogen)
Warning: poorly guessed coordinates for 8 atoms (2 non-hydrogen):
Warning: poorly guessed coordinate for atom HT1 MET:1 U
Warning: poorly guessed coordinate for atom HT2 MET:1 U
Warning: poorly guessed coordinate for atom HT3 MET:1 U
Warning: poorly guessed coordinate for atom HG2 PRO:19 U
Warning: poorly guessed coordinate for atom HG2 PRO:37 U
Warning: poorly guessed coordinate for atom HG2 PRO:38 U
Warning: poorly guessed coordinate for atom OT1 GLY:76 U
Warning: poorly guessed coordinate for atom OT2 GLY:76 U
Info: writing pdb file ubq.pdb
Info: Atoms with guessed coordinates will have occupancy of 0.0.
Info: pdb file complete.
write: psf is not logged in on ubq.psf
child process exited abnormally
vmd >

I am also getting "invalid command" when using -dispdev at the command
line. Any suggestions on how to proceed would be greatly appreciated.

Thank you.

Matt