VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Mon May 07 2007 - 08:36:50 CDT

On Mon, 7 May 2007, Himanshu Khandelia wrote:

HK> Hi,
HK>
HK> I am trying to use bigdcd.tcl, but vmd stops after reading one frame with
HK> no errors. My trajectory does have multiple frames, and was obtained by
HK> merging using catdcd. I cannot figure out what is wrong.
HK>
HK> I am implementing the above script using
HK>
HK> vmd -dispdev text < myscript.tcl

please try running:

vmd -dispdev text -e myscript.tcl

and then wait until you see 'bigdcd done' before typing 'quit'
or put 'after idle { quit }' at the end of your script.

to explain: bigdcd loads the trajectory in background
so you have to wait until bigdcd is done, before you
can quite the tcl interpreter.

cheers,
   axel.

HK>
HK> Here is the exact output:
HK>
HK> ####################################
HK> Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
HK> Info) http://www.ks.uiuc.edu/Research/vmd/
HK> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
HK> Info) Please include this reference in published work using VMD:
HK> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
HK> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
HK> Info) -------------------------------------------------------------
HK> Info) Multithreading available, 2 CPUs detected.
HK> psfplugin) Detected a Charmm31 PSF file
HK> Info) Using plugin psf for structure file proteincharmm.psf
HK> Info) Analyzing structure ...
HK> Info) Atoms: 15228
HK> Info) Bonds: 15436
HK> Info) Residues: 1008
HK> Info) Waters: 0
HK> Info) Segments: 5
HK> Info) Fragments: 8 Protein: 4 Nucleic: 0
HK> 0
HK> Info) Using plugin pdb for coordinates from file protein.pdb
HK> Info) Finished with coordinate file protein.pdb.
HK> dcdplugin) detected standard 32-bit DCD file of native endianness
HK> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
HK> Info) Using plugin dcd for coordinates from file protein.dcd
HK> this is frame number 1
HK> Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
HK> Info) Exiting normally.
HK> ####################################
HK>
HK> Thanks very much !
HK>
HK> -Himanshu
HK> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.