Re: Fatal error in configuration file

From: Chris Harrison (char_at_ks.uiuc.edu)
Date: Thu Feb 05 2009 - 20:27:23 CST

Corey,

The dot after your cutoff value is not a problem and should not crash of
NAMD. Assuming whatever editor you used does not place "^M" at each
end-of-line (as do many MSWin based editors); I strongly suggest you
carefully look that there is not *empty white space immediately** after* the
dot. This is very likely the cause of your crash and not an uncommon source
of frustration. I suggest you do the same inspection for empty white space
after your "switchdist" as well .... perhaps it would be a good idea to do
it for all lines in your config file that terminate in a number. :)

C.

--
Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801
char_at_ks.uiuc.edu                            Voice: 217-244-1733
http://www.ks.uiuc.edu/~char               Fax: 217-244-6078
On Wed, Feb 4, 2009 at 10:12 PM, BIN ZHANG <zhngbn_at_gmail.com> wrote:
> You should delete the dot "." after the number.
> Somehow this can not be understood by NAMD Binary on mac.
>
> Best,
> Bin
>
>
>
> On Feb 4, 2009, at 7:05 PM, Corey Fugate wrote:
>
>         I have been going through the NAMD tutorial on my Mac OS 10.5.  I
>> already posted for help on the Tutorial sight, and the response I received
>> suggested that I direct my question to the NAMD-l.
>>        I'm trying to run the ubq_ws_eq.conf file from the 1-2-sphere
>> directory.  I receive the following message in the terminal -
>>
>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>> Reason: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>>
>> Charm++ fatal error:
>> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>>
>> Abort trap
>>
>>
>> I have not manipulated the config file.  I tried the config in the 1-3-box
>> directory and receive the same error.  The log file for the execution of
>> ubq_ws_eq.conf is below
>>
>>
>> Charm++: standalone mode (not using charmrun)
>> Charm++: scheduler running in netpoll mode.
>> Info: NAMD 2.6 for MacOSX-i686
>> Info:
>> Info: Please visit http://www.ks.uiuc.edu/Research/namd/
>> Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
>> Info:
>> Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
>> Info: in all publications reporting results obtained with NAMD.
>> Info:
>> Info: Based on Charm++/Converse 50900 for net-darwin-x86-smp
>> Info: Built Wed Aug 30 12:54:31 CDT 2006 by jim on juneau.ks.uiuc.edu
>> Info: 1 NAMD  2.6  MacOSX-i686  1
>> dhcp-128-171-32-170.bilger.hawaii.edu  Corey
>> Info: Running on 1 processors.
>> Info: 86012 kB of memory in use.
>> Info: Memory usage based on ps
>> Info: Configuration file is ubq_ws_eq.conf
>> TCL: Suspending until startup complete.
>> ERROR: Could not understand units '.' in option 'cutoff = 12.
>> ERROR: 'cutoff' was set to 0 but it should be positive
>> ERROR: Could not understand units '.' in option 'switchdist = 10.
>> ERROR: 'switchdist' was set to 0 but it should be positive
>> FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
>>
>>
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> -------------------------------------------------------------
> The tree of liberty must be refreshed from time to time with the blood of
> patriots and tyrants.
>
>

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