From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Tue Aug 14 2007 - 07:01:28 CDT
Anyone, please ?
Please pardon my impatience
On 8/13/07, maria goranovic <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/
> 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.
> 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
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:05 CST