VMD-L Mailing List

From: Matthew Bick (bickm_at_mail.rockefeller.edu)
Date: Mon May 30 2011 - 14:03:30 CDT

Thank you all for your responses. Yes, it was indeed the fact that I
had a space between write and psf in the ubq.pgn file. Quite
embarrassing :-). Guess I should have checked a fourth time.

Matt

On May 30, 2011, at 2:15 PM, Axel Kohlmeyer wrote:

> 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.