VMD-L Mailing List

From: KK R (kkres14_at_gmail.com)
Date: Wed Jul 15 2015 - 11:30:02 CDT

Hi John,
Thanks very much for your suggestion. I edited the script as below:

source bigdcd.tcl
package require pbctools
proc nwc { frame } {
global sel nf text
for { set i 1 } { $i < $nf } { incr 1 } {
$sel frame $i
$sel [pbc unwrap -first 0]
puts $text
$sel [pbc wrap -centersel "protein" -center com -compound residue -all]
puts $text
$sel [animate write dcd Wrapped.dcd]
puts $text
}
$sel delete
}
mol load psf ../Mypsf.psf
set sel [atomselect top all]
set nf [molinfo top get numframes]
set text "DONE"
bigdcd nwc Mydcd.dcd
bigdcd_wait
quit

Running this script gives following log output.

Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
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, 24 CPUs detected.
Info) Free system memory: 28139MB (87%)
Warning) Detected a mismatch between CUDA runtime and GPU driver
Warning) Check to make sure that GPU drivers are up to date.
Info) No CUDA accelerator devices available.
Info) Dynamically loaded 2 plugins in directory:
Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile

/home/kkr/pbctools-2.5
2.6
2.6
psfplugin) Detected a Charmm31 PSF file
psfplugin) Detected a Charmm31 PSF EXTEnded file
Info) Using plugin psf for structure file ../Mypsf.psf
Info) Analyzing structure ...
Info) Atoms: 104687
Info) Bonds: 104375
Info) Angles: 94547 Dihedrals: 101453 Impropers: 1401 Cross-terms: 346
Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
Info) Residues: 22866
Info) Waters: 22140
Info) Segments: 6
Info) Fragments: 22520 Protein: 1 Nucleic: 0
0
atomselect0
0
DONE
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 Mydcd.dcd
bigdcd aborting at frame 1
can't unset "upproc_var_atomselect0": no such variable
bigdcd_done
after#0
Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
Info) Exiting normally.

Please help!

Thanks.

Roy

On Tue, Jul 14, 2015 at 10:26 AM, John Stone <johns_at_ks.uiuc.edu> wrote:

> Hi,
> There appear to be syntax errors in several places in your script.
> You have "waitfor all" in several places where it doesn't belong, in
> particular at the end of some atom selection commands. To debug your
> script, you may want to add some calls to "puts" at various points and
> that will help you determine where the error occured (after the error(s),
> subsequent puts calls won't show up any more).
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Jul 08, 2015 at 12:52:47PM -0500, KK R wrote:
> > Dear VMD users,
> > I am trying to use bigdcd for wrapping, unwrapping and writeing dcd
> file
> > using VMD text mode with the command:
> >
> > vmd -dispdev text -e Script.tcl
> >
> > Script.tcl is:
> >
> > source bigdcd.tcl
> > package require pbctools
> > proc nwc { frame } {
> > global sel nf
> > for { set i 1 } { $i < $nf } { incr 1 } {
> > $sel frame $i
> > $sel [pbc unwrap -first 0] waitfor all
> > $sel [pbc wrap -centersel "protein" -center com -compound residue
> -all]
> > waitfor all
> > $sel [animate write dcd Wrappeddcd.dcd] waitfor all
> > }
> > return
> > }
> > mol load psf Mypsf.psf
> > set sel [atomselect top all]
> > set nf [molinfo top get numframes]
> > bigdcd nwc Mydcd.dcd
> > bigdcd_wait
> > quit
> >
> > However, it is doing nothing. I am not able to grab loophole(s) in my
> tcl
> > script despite going through VMD discussion forum.
> >
> > Any suggestion would be appreciated.
> >
> > Thanks in advance!
> >
> > kkr
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/
>