VMD-L Mailing List

From: Himanshu Khandelia (hkhandel_at_memphys.sdu.dk)
Date: Mon May 07 2007 - 04:42:10 CDT

Hi,

I am trying to use bigdcd.tcl, but vmd stops after reading one frame with
no errors. My trajectory does have multiple frames, and was obtained by
merging using catdcd. I cannot figure out what is wrong.

Here is the input script:

####################################
source ~/ANALYSIS/bigdcd.tcl

proc test { frame } {
  puts "this is frame number $frame"
}
mol load psf proteincharmm.psf
animate read pdb protein.pdb
bigdcd test protein.dcd
####################################

I am implementing the above script using

vmd -dispdev text < myscript.tcl

Here is the exact output:

####################################
Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
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, 2 CPUs detected.
psfplugin) Detected a Charmm31 PSF file
Info) Using plugin psf for structure file proteincharmm.psf
Info) Analyzing structure ...
Info) Atoms: 15228
Info) Bonds: 15436
Info) Residues: 1008
Info) Waters: 0
Info) Segments: 5
Info) Fragments: 8 Protein: 4 Nucleic: 0
0
Info) Using plugin pdb for coordinates from file protein.pdb
Info) Finished with coordinate file protein.pdb.
dcdplugin) detected standard 32-bit DCD file of native endianness
dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
Info) Using plugin dcd for coordinates from file protein.dcd
this is frame number 1
Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
Info) Exiting normally.
####################################

Thanks very much !

-Himanshu