VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Jun 03 2015 - 16:04:13 CDT

Hi Josh

"[measure rgyr $sel]" was a refuse from using rgyr.tlc as a template. That
deleted, it works. No excuse for having not paid attention enough to the
error message on the terminal.

thanks indeed
francesco

On Wed, Jun 3, 2015 at 9:03 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> Read the error message again. For once the TCL error message is quite
> clear, you told it to look for a variable "sel", but you define a "sel1"
> and "sel2".
> -Josh
>
>
> On 6/3/15 12:08 PM, Francesco Pietra wrote:
>
> Hello:
> I could successfully run centermass, rmsd and rgyr with bigdcd.tcl and
> vmd in text mode. In contrast, with distance.tcl I was unsuccessful.
> The distance.tcl script reads
>
> source bigdcd.tcl
>
> proc distance { frame } {
> global all sel1 sel2 coord1 coord2 outfile
> set coord1 [lindex [$sel1 get {x y z}] 0]
> set coord2 [lindex [$sel2 get {x y z}] 0]
> puts $outfile "$frame: [vecdist $coord1 $coord2]" "[measure rgyr $sel]"
> }
> set outfile [open distance.dat w];
> # set mol [mol new protein.psf waitfor all]
> set mol [mol new blg.psf waitfor all]
> # mol addfile protein.pdb type pdb waitfor all
> mol addfile blg.pdb type pdb waitfor all
> # set sel1 [atomselect $mol "protein and resid 1 and alpha"]
> # set sel2 [atomselect $mol "protein and resid 2 and alpha"]
> set sel1 [atomselect $mol "protein and resid 34 and alpha"]
> set sel2 [atomselect $mol "protein and resid 36 and alpha"]
> # bigdcd distance eq-0.dcd eq-1.dcd
> bigdcd distance blg.dcd
> bigdcd_wait
> close $outfile
>
> The terminal output reads:
>
> $ vmd -e distance.tcl -dispdev none > distance.txt
> bigdcd aborting at frame 1
> can't read "sel": no such variable
>
> while distance.txt reads:
>
> Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
> Info) http://www.ks.uiuc.edu/Research/vmd/
> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ks.uiuc.edu_Research_vmd_&d=AwMFaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=zFfoK61upjM5BwyoRAsX8dLq7rwWm8aw7r7dqtjgcCE&m=g6p7HdYglOj0-ooifNizxiz58OT7_hj4SD4MtUs-Vqo&s=-pJlm3G--yiCmhSxKqfdhSBERZOYaO3oM3-V46EqQZs&e=>
>
> 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, 4 CPUs detected.
> Info) Free system memory: 7074MB (89%)
> 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
> loading bigdcd...
> bigdcd loaded...
> file4
> Info) Using plugin psf for structure file blg.psf
> psfplugin) no cross-terms defined in PSF file.
> Info) Analyzing structure ...
> Info) Atoms: 25366
> Info) Bonds: 17736
> Info) Angles: 12120 Dihedrals: 6544 Impropers: 384 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 7802
> Info) Waters: 7644
> Info) Segments: 3
> Info) Fragments: 7651 Protein: 1 Nucleic: 0
> 0
> Info) Using plugin pdb for coordinates from file blg.pdb
> Info) Finished with coordinate file blg.pdb.
> 0
> atomselect0
> atomselect1
> dcdplugin) detected standard 32-bit DCD file of native endianness
> dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)
> dcdplugin) Warning: DCD header claims 140 frames, file size indicates
> there are actually 141 frames
> Info) Using plugin dcd for coordinates from file blg.dcd
> bigdcd_done
> after#0
> vmd > Info) Finished with coordinate file blg.dcd.
>
> and distance.dat is empty.
>
> Thanks a lot for pointing out what is wrong in the tcl script
>
> francesco pietra
>
>
>