AW: NAMD failed to read AMBER parm file

From: Norman Geist (
Date: Fri Nov 09 2012 - 01:37:25 CST

This is just a filename/path issue. Check if you set the right name for the
prmtop. You see this, because namd searches for all kinds of files with your
supplied filename with additional extensions like gz and Z.


Norman Geist.


Von: [] Im Auftrag
von Sneha Menon
Gesendet: Freitag, 9. November 2012 06:19
Betreff: namd-l: NAMD failed to read AMBER parm file


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

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:22:14 CST