From: Pang, Yui Tik (
Date: Tue Nov 17 2020 - 20:36:02 CST

Hi Easchan,

As the error suggested, NAMD cannot find the file eq1.xsc . Are you sure you have copy the restart files (I guess they are eq1.coor, eq1.vel and eq1.xsc) to the 2_calibrate folder?


From: Eashan C<>
Sent: Tuesday, November 17, 2020 8:00 PM
Subject: vmd-l: extended system file not found


Ive been trying to follow the bionanotechnology tutorial to simulate solid state nanopores, so far ive gone through the exact same steps as specified in the tutorial.

During the force field calibration, i am required to run namd2 on eq2.namd in the 2_calibrate folder for the tutorial.

However i get an error along the lines of extended system file not found. The log file contains the following-

Charm++: standalone mode (not using charmrun)
Converse/Charm++ Commit ID: v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-Dec-08-28969
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (8-way SMP).
Charm++> cpu topology info is gathered in 0.000 seconds.
Info: NAMD 2.10 for MacOSX-x86_64-multicore
Info: Please visit
Info: for updates, documentation, and support information.
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info: Based on Charm++/Converse 60601 for multicore-darwin-x86_64
Info: Built Tue Dec 9 15:31:59 CST 2014 by jim on<>
Info: 1 NAMD 2.10 MacOSX-x86_64-multicore 1 Eashans-MacBook-Pro.local e
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00251102 s
Info: 4210.95 MB of memory in use based on ps
Info: Configuration file is eq2.namd
Info: Working in the current directory /Users/e/VMD/bionano-tutorial-files/2_calibrate
TCL: Suspending until startup complete.
FATAL ERROR: Unable to open extended system file.

[0] Stack Traceback:
  [0:0] 0 namd2 0x00000001006ff9fd CmiAbort + 77
  [0:1] 1 namd2 0x000000010007a9ef _Z8NAMD_diePKc + 79
[0] Stack Traceback:
  [0:0] 0 namd2 0x00000001006fdf79 charmrun_abort + 249
  [0:1] 1 namd2 0x00000001006ffa38 CmiAbort + 136
  [0:2] 2 namd2 0x000000010007a9ef _Z8NAMD_diePKc + 79

Can anyone help me out as to where I might be going wrong? I have gone through the tutorial exactly as specified so far, going as far as to directly copy the commands from the pdf, rather than type them out on my most recent try.

Eashan Chopde
Undergrad, BITS Pilani