From: John Stone (
Date: Wed Mar 05 2008 - 12:25:42 CST

  The error message you're getting, specifically the line beginning with
"FATAL ERROR" looks like it's coming from NAMD and not from VMD. The
subsequent stack traceback is coming from Charm++ which is part of NAMD,
so I think that the part of your script you need to check closely is whatever
portion is running NAMD.

Indeed I did install VMD on the BigRed machine at Indiana, but there's
nothing particularly special about it other than that I compiled it on
their machine. You should be able to run everything in your own VMD
that you can run on the BigRed machine at Indiana, though if your scripts
call other programs/packages, you'll have to check on those individually.

  John Stone

On Wed, Mar 05, 2008 at 12:59:20PM -0500, Corenflos, Steven Charles wrote:
> 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.
> Thanks,
> -Steve
> Info) VMD for LINUXAMD64, version 1.8.6 (April 6, 2007)
> Info)
> 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]

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