NAMD failed to read AMBER parm file

From: Sneha Menon (
Date: Thu Nov 08 2012 - 23:19:00 CST

Dear all,

I encountered a problem while trying to run NAMD 2.8 using Amber
forcefield. I created the prmtop and inpcrd files using AmberTools 1.2 and
used them to run NAMD.
However it failed with the error - ' FATAL ERROR: Failed to read AMBER
parm file! '
The end part of the output file is as follows:

Reading parm file (prp_3sod_11238.prmtop) ...
Command = zcat prp_3sod_11238.prmtop.Z
Filename.Z = prp_3sod_11238.prmtop.Z
Command = gzip -d -c prp_3sod_11238.prmtop.gz
Filename.gz = prp_3sod_11238.prmtop.gz
FATAL ERROR: Failed to read AMBER parm file!
[0] Stack Traceback:
  [0:0] CmiAbort+0x7b [0xbf1bd9]
  [0:1] _Z8NAMD_diePKc+0x62 [0x535542]
  [0:2] _
ZN9NamdState14configListInitEP10ConfigList+0xcb4 [0x9fc42a]
  [0:3] _ZN9ScriptTcl9initcheckEv+0x5e [0xa7c342]
  [0:4] _ZN9ScriptTcl3runEv+0x66 [0xa77eec]
  [0:5] _Z18after_backend_initiPPc+0x4fd [0x539d7d]
  [0:6] main+0x3a [0x53984a]
  [0:7] __libc_start_main+0xf4 [0x3d8461d994]
  [0:8] _ZNSt8ios_base4InitD1Ev+0x4a [0x534e3a]

I've read in the archive about a similar error, which suggested deleting
the sections under the flags 'SCEE_SCALE_FACTOR ' and 'SCNB_SCALE_FACTOR '
from the prmtop file.
I checked for the same, but my prmtop file doesn't contain these sections.

What could be the possible error? Could you help me?

Sneha Menon

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