From: Sneha Menon (sneha.menon15_at_gmail.com)
Date: Sat Nov 17 2012 - 03:44:08 CST
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 <norman.geist_at_uni-greifswald.de
> 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] *Im
> Auftrag von *Sneha Menon
> *Gesendet:* Freitag, 9. November 2012 06:19
> *An:* 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 sections.
> What could be the possible error? Could you help me?
> Sneha Menon****
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