VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon May 30 2011 - 13:15:58 CDT

On Mon, May 30, 2011 at 1:32 PM, Matthew Bick
<bickm_at_mail.rockefeller.edu> wrote:
> 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

the command is "writepsf" not "write psf".
the blank makes a big difference. "write" is a tcl primitive.

i guess you should have checked your file one time more. ;-)

cheers,
     axel.

> 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 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.