VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat May 30 2015 - 10:41:21 CDT

Hi,
  It looks to me as through your script is failing to load bigdcd.tcl,
and that is why it is aborting. I would suggest that you put the
bigdcd.tcl script in the working directory, or that ou modify your code
to use the full pathname to the bigdcd.tcl script.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sat, May 30, 2015 at 05:19:32PM +0200, Francesco Pietra wrote:
> Hello:
>
> I could calculate the radius of gyration on my computer (VMD 1.9.1) with
> short, test files, following command
>
> vmd -e rgyr.tcl -dispdev none > rgyr_npt35.tx
>
> The same tlc script failed to perform on a long file at the computing
> center, following commands
>
> module load profile/advanced vmd
>
> vmd -e rgyr.tcl -dispdev none > rgyr_npt35.txt
>
>
>
> The tlc script reads:
>
> # calculates radius of gyration using bigdcd
>
> # run with vmd in text mode
> #
>
> source bigdcd.tcl
>
> proc gyration { frame } {
> global ref sel all outfile
> $all move [measure fit $ref $sel]
> puts "$frame: [measure rgyr $sel]"
> puts $outfile "[measure rgyr $sel]"
> }
> set mol [mol addfile XAN_O2-out_watbox_isotonic.pdb type pdb waitfor all]
> set all [atomselect $mol all]
> set ref [atomselect $mol "protein and backbone and noh" frame 0]
> set sel [atomselect $mol "protein and backbone and noh"]
> set outfile [open gyration.dat w]
> bigdcd gyration dcd npt-35.dcd
> bigdcd_wait
> close $outfile
>
>
> Permission for the tcl script
>
> -rw-r--r--
>
> I also tried by giving execute permission, although it should be unnecessary
>
> -rwxr-xr-x
>
>
> The wrong rgyr_npt35.txt from the computing center reads:
>
> Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
> 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, 16 CPUs detected.
> Info) Free system memory: 115938MB (90%)
> Info) Creating CUDA device pool and initializing hardware...
> Info) Detected 2 available CUDA accelerators:
> Info) [0] Tesla K40m 15 SM_3.5 @ 0.75 GHz, 11GB RAM, KTO, AE2, ZCP
> Info) [1] Tesla K40m 15 SM_3.5 @ 0.75 GHz, 11GB RAM, KTO, AE2, ZCP
> Info) Detected 2 available TachyonL/OptiX ray tracing accelerators
> Info) Dynamically loaded 2 plugins in directory:
> Info) /cineca/prod/tools/vmd/1.9.2/binary/lib/vmd/plugins/LINUXAMD64/molfile
> too many nested evaluations (infinite loop?)
> Info) Using plugin pdb for structure file XAN_O2-out_watbox_isotonic.pdb
> Info) Using plugin pdb for coordinates from file
> XAN_O2-out_watbox_isotonic.pdb
> Info) Determining bond structure from distance search ...
> Info) Finished with coordinate file UOX_XAN_O2-out_watbox_isotonic.pdb.
> Info) Analyzing structure ...
> Info) Atoms: 187233
> Info) Bonds: 131246
> Info) Angles: 0 Dihedrals: 0 Impropers: 0 Cross-terms: 0
> Info) Bondtypes: 0 Angletypes: 0 Dihedraltypes: 0 Impropertypes: 0
> Info) Residues: 57547
> Info) Waters: 56031
> Info) Segments: 37
> Info) Fragments: 56371 Protein: 4 Nucleic: 0
> 0
> atomselect0
> atomselect1
> atomselect2
> file28
> invalid command name "bigdcd"
> invalid command name "bigdcd_wait"
> vmd > Info) VMD for LINUXAMD64, version 1.9.2 (December 29, 2014)
> Info) Exiting normally.
>
> I wonder whether
> means that the plugins are not loaded.
>
>
> The same failure was met with related tcl scripts for calculationg the
> center of mass and the rmsd, both running correctly on my computer.
>
> Thanks for advice
> francesco pietra 

-- 
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/