Can you use NAMD 2.9?
It's likely a line in the parm file that was added by AMBER and hadn't been
coded in. I recall there is such a line, I think in the parm file there is
a section for SCEE and SCNB. NAMD uses the same value for all atoms, but
AMBER can have unique values for each atom. If you must use 2.8, try
looking through your parm file for those headers, and delete those lines (I
think they come next to one another).
~Aron
On Wed, Nov 7, 2012 at 7:25 AM, Sneha Menon <sneha.menon15.gmail.com> wrote:
> 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'm unable to figure out the error. Could you help me out?
> I've attached the top, coor and the output files. PFA.
>
> Regards,
> Sneha Menon
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Wed Nov 07 2012 - 08:30:03 PST
