VMD-L Mailing List

From: Bennion, Brian (bennion1_at_llnl.gov)
Date: Fri May 29 2015 - 10:48:54 CDT

You need to remove the dollar sign from he set mol [] command.
Brian


From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Francesco Pietra
Sent: Friday, May 29, 2015 7:36 AM
To: VMD Mailing List
Subject: vmd-l:

Hello
What is wrong in my centermass.tcl script below? (taken from the web)



# This computes the center of mass for each frame in the DCD file.
#
source bigdcd.tcl

proc mycenter { frame } {
  global all
    puts "$frame: [measure center $all weight mass]"
}
set $mol [mol new blg.psf type psf waitfor all]
set all [atomselect $mol all]
$all global
bigdcd mycenter auto blg.dcd
quit


as command

vmd -e centermass.tcl -dispdev none > centermass.out

reports:

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<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, 4 CPUs detected.
Info) Free system memory: 7209MB (90%)
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
can't read "mol": no such variable
can't read "mol": no such variable
can't read "all": no such variable
molinfo: get: no molecule exists with id -1
Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
Info) Exiting normally.
vmd >

Is blg.pdb lacking? These blg files work finely with the related rmsd script from the same source.
Thanks
francesco pietra