From: Joachim Hein (j.hein_at_ed.ac.uk)
Date: Fri May 29 2009 - 11:07:56 CDT
is your NAMD build with TCL? If not the ; used in the configuration
files will confuse the hell out of it. Removing the ; will cure this
for many input files, though not having TCL will use you some NAMD
Hope this helps.
Yogesh Aher wrote:
> Dear all,
> While going through the tutorial, when I gave command : ./namd2
> ubq_wb_eq.conf > ubq_wb_eq.log
> Got the following error:/
> Info: Based on Charm++/Converse 60102 for mpi-linux
> Info: Built Mon May 18 13:51:37 CEST 2009 by abc on abc-desktop
> Info: 1 NAMD 2.6 Linux-i686-MPI 1 abc-desktop abc
> Info: Running on 1 processors.
> Info: 1385 kB of memory in use.
> Info: Memory usage based on CmiMemoryUsage
> Info: Configuration file is ubq_wb_eq.conf
> ERROR: Could not understand units ';' in option 'timestep = 2.0 ;
> ERROR: Expecting value and optional units for option 'temperature'
> ERROR: Expecting only a number for 'restartfreq' input, got: 500 ;
> ERROR: ParseOptions can't understand 'on ;' for the
> ERROR: Boolean variable 'Langevin'
> ERROR: ParseOptions can't understand 'yes ;' for the
> ERROR: Boolean variable 'useGroupPressure'
> ERROR: Could not understand units ';' in option 'LangevinPistonTarget =
> 1.01325 ;
> ERROR: Expecting value and optional units for option 'LangevinPistonTemp'
> ERROR: 'LangevinPistonTemp' was set to 0 but it should be positive
> Warning: The following variables were set in the
> Warning: configuation file but were not needed
> Warning: langevinTemp
> Warning: langevinDamping
> Warning: langevinHydrogen
> ERROR: The following variables were set in the
> ERROR: configuration file but are NOT VALID
> ERROR: run
> ERROR: reinitvels
> ERROR: minimize
> ERROR: set
> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>  Stack Traceback:
>  CmiAbort+0x2f [0x83af99e]
>  _Z8NAMD_diePKc+0x5c [0x8134a5e]
>  _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0x6b
>  _ZN13SimParametersC1EP10ConfigListRPc+0x115 [0x82a7117]
>  _ZN9NamdState14configListInitEP10ConfigList+0x70 [0x82a57ee]
>  _ZN9ScriptTcl9initcheckEv+0x33 [0x82e0299]
>  _ZN9ScriptTcl3runEPc+0x95 [0x82e035b]
>  main+0x27c [0x8137164]
>  __libc_start_main+0xe0 [0xb7c9e450]
>  namd2 [0x8133bf1]/
> Am I missing something?
> Please let me know, how to come out of this problem.
> Thanking you,
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