From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Aug 14 2007 - 09:02:49 CDT
Maria,
have you tried running this same script in an interactive VMD session?
Are you starting vmd with -eofexit? You might want to try without it, eg,
vmd -dispdev text -e myscript.tcl
Peter
maria goranovic wrote:
> Anyone, please ?
>
> Please pardon my impatience
>
> On 8/13/07, *maria goranovic* <mariagoranovic_at_gmail.com
> <mailto:mariagoranovic_at_gmail.com> > wrote:
>
> Hi All,
>
> I have a peculiar problem while working with bigdcd.tcl which I
> downloaded off the website, and stored in the directory
> ~/NAMD_SCRIPTS. Here is the problem:
>
> The number of frames that is accessed by my procedure using bigdcd
> is the same as the number of new line characters that appear after
> the last line in the tcl script below. Why would this happen ?
>
> Here is the script with 2 example input scripts and corresponding
> outputs. Please note that the 2 input scripts only differ in the
> number of empty lines after the last line of the script.
>
> INPUT1:
> #########################3
> source ~/NAMD_SCRIPTS/bigdcd.tcl
> mol load pdb waterprotcharmm.pdb
> proc displacement {frame} {
> puts $frame
> }
>
> bigdcd displacement waterprot-10k.dcd
> #########################3
>
> OUTPUT1:
>
> #########################3
> Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> <http://www.ks.uiuc.edu/Research/vmd/>
> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
> <mailto: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.
> after#0
> psfplugin) Detected a Charmm31 PSF file
> Info) Using plugin psf for structure file waterprotcharmm.psf
> Info) Analyzing structure ...
> Info) Atoms: 65594
> Info) Bonds: 65802
> Info) Residues: 17818
> Info) Waters: 16810
> Info) Segments: 9
> Info) Fragments: 16818 Protein: 4 Nucleic: 0
> 0
> 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 waterprot-10k.dcd
> 1
> Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
> Info) Exiting normally
>
> INPUT2:
> #########################3
> source ~/NAMD_SCRIPTS/bigdcd.tcl
> mol load pdb waterprotcharmm.pdb
> proc displacement {frame} {
> puts $frame
> }
>
> bigdcd displacement waterprot-10k.dcd
>
>
>
> #########################3
>
> OUTPUT2: (same as output 1, except that more frames are accessed
> #########################3
> ...
> ...
> 1
> 2
> 3
> 4
> Info) VMD for LINUX, version 1.8.5 (August 25, 2006)
> Info) Exiting normally
> #########################3
>
>
>
> Maria G.
> Technical University of Denmark
> Copenhagen
>
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
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