From: Felipe Merino (felipe.merino_at_mpi-muenster.mpg.de)
Date: Sat Nov 17 2012 - 10:48:12 CST
NAMD 2.8 cannot read the topology files generated by AmberTools 1.5 or
higher. This is because it contains thwo sections (SCEE and SCNB) which
cannot be parsed. Either you remove them for 2.8 or you use NAMD 2.9 for
On 11/17/2012 10:44 AM, Sneha Menon wrote:
> I checked the file path, it seems alright. Also I tried using a higher
> version- AmberTools12. But the problem still persists.
> - Sneha Menon
> On Fri, Nov 9, 2012 at 1:07 PM, Norman Geist
> <mailto:norman.geist_at_uni-greifswald.de>> wrote:
> 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:*owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu>
> <mailto:owner-namd-l_at_ks.uiuc.edu>] *Im Auftrag von *Sneha Menon
> *Gesendet:* Freitag, 9. November 2012 06:19
> *An:* namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
> *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!
>  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
> What could be the possible error? Could you help me?
> Sneha Menon
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