From: nealec (
Date: Fri Dec 12 2014 - 20:17:09 CST

Dear users:

I would like to use the chirality and cispeptide plugins to vmd in text
mode. However, I am having difficulty.

Everything works fine if I open it with the visualization and then, in
the tkconsole window:

loading history file ... 13 events added
Main console display active (Tcl8.5.6 / Tk8.5.6)
(GET_STRUCT) 14 % chirality
Usage: chirality <command> [args...]
   check -- identify chirality errors
   list -- list identified chirality errors
   minimize -- fix chirality errors using energy minimization
   move -- move hydrogen atom to fix chirality
   reset -- reinitialize plugin state
   restrain -- generate NAMD extrabonds file to prevent chirality changes
   show -- visualize identified chirality errors

> Main< (GET_STRUCT) 15 % cispeptide
Usage: cispeptide <command> [args...]
   check -- identify cis peptide bonds
   list -- list identified cis peptide bonds
   minimize -- fix cis peptide bonds using energy minimization
   move -- move specified atom to convert to trans
   reset -- reinitialize plugin state
   restrain -- generate NAMD extrabonds file to restrain peptide bonds
   set -- define how to modify a given cis peptide bond
   show -- visualize identified cis peptide bonds


However, when I try from the command line on the same computer:

[nealec_at_pegasus GET_STRUCT]$ vmd -dispdev text
Info) VMD for LINUXAMD64, version 1.9.1 (February 1, 2012)
Info) Email questions and bug reports to
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: 1489MB (37%)
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/vmd/lib/plugins/LINUXAMD64/molfile
/home/nealec/exe/BENDIX /usr/local/vmd/lib/scripts/tcl8.5
/usr/local/vmd/lib/scripts /usr/local/vmd/lib
/usr/local/vmd/lib/scripts/vmd /usr/local/vmd/lib/plugins/LINUXAMD64/tcl
The bendix package could not be loaded:

vmd > chirality
invalid command name "chirality"
vmd > cispeptide
invalid command name "cispeptide"
vmd >

Is there any way to get these two plugins to work from the command line
(i.e., on a cluster)? Note that I also tried "vmd -dispdev win" on a
cluster, got the same access to the command line, and again these
plugins were not usable.

Thank you for your help,