From: Joachim Hein (j.hein_at_ed.ac.uk)
Date: Fri May 29 2009 - 11:40:41 CDT
Joachim Hein wrote:
> Hi,
>
> 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
this was meant to read "loose you some NAMD functionality". -Sorry-
Joachim
> functionality.
>
> Hope this helps.
> Joachim
>
> 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
>> [0] Stack Traceback:
>> [0] CmiAbort+0x2f [0x83af99e]
>> [1] _Z8NAMD_diePKc+0x5c [0x8134a5e]
>> [2]
>> _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0x6b
>> [0x82fb7dd]
>> [3] _ZN13SimParametersC1EP10ConfigListRPc+0x115 [0x82a7117]
>> [4] _ZN9NamdState14configListInitEP10ConfigList+0x70 [0x82a57ee]
>> [5] _ZN9ScriptTcl9initcheckEv+0x33 [0x82e0299]
>> [6] _ZN9ScriptTcl3runEPc+0x95 [0x82e035b]
>> [7] main+0x27c [0x8137164]
>> [8] __libc_start_main+0xe0 [0xb7c9e450]
>> [9] namd2 [0x8133bf1]/
>>
>> Am I missing something?
>> Please let me know, how to come out of this problem.
>>
>> Thanking you,
>> Y.
>>
>>
>
>
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