From: Joachim Hein (j.hein_at_ed.ac.uk)
Date: Fri May 29 2009 - 11:40:41 CDT
Joachim Hein wrote:
> 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-
> 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]
>>  _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,
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:52 CST