From: Corenflos, Steven Charles (
Date: Wed Mar 05 2008 - 11:59:20 CST

I'm getting an error message running a TCL script that's calling the program VMD. Trying to track down the source of the problem is frustrating me to no end. I know that these same scripts are working fine on a university-owned research server (which I heard the VMD developers kindly installed VMD on themselves), but when we try to use them on our own server we run into this problem. Here's the relevant portion of the output. If anyone knows where to direct me for some help with this it would be greatly appreciated and save me years of therapy down the road.


Info) VMD for LINUXAMD64, version 1.8.6 (April 6, 2007)
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, 8 CPUs detected.
Info) Free system memory: 13051MB (81%)
AMA) ----------------------------ama_cycle.tcl---------------------------------
TCL: error reading output from command: interrupted system call
FATAL ERROR: error reading output from command: interrupted system call
    while executing
"exec vmd -dispdev text -e ${amadir}/ama_cycle.tcl | tee -a ${molname}.log"
    invoked from within
"time {exec vmd -dispdev text -e ${amadir}/ama_cycle.tcl | tee -a ${molname}.log}"
    invoked from within
"if {1} {

set t $t_start
set cycle 0
set fT [open $Tfile w]; puts "AMA) Open file ${Tfile} for saving OP timestep information..."
    (file "/home/long/AMA/ama_namd.tcl" line 40)
    invoked from within
"source ${amadir}/ama_namd.tcl"
    (file "1cwp-vmd-H.conf" line 169)
Stack Traceback:
  [0] CmiAbort+0x33 [0x7f17f5]
  [1] _Z8NAMD_diePKc+0x62 [0x4b2f62]
  [2] _ZN9ScriptTcl3runEPc+0x54 [0x6fb75e]
  [3] main+0x21b [0x4b6743]
  [4] __libc_start_main+0xf4 [0x2b6dd6cb4b44]
  [5] _ZNSt8ios_base4InitD1Ev+0x3a [0x4b28da]