Re: Fatal error in configuration file

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Thu Feb 05 2009 - 22:28:26 CST

That makes more sense. ;-)

Thanks,
Bin

On Feb 5, 2009, at 6:27 PM, Chris Harrison wrote:

> 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
>
>
>
>
>
>
>
>
>
>
> -------------------------------------------------------------
> The tree of liberty must be refreshed from time to time with the
> blood of patriots and tyrants.
>
>

-------------------------------------------------------------
The tree of liberty must be refreshed from time to time with the blood
of patriots and tyrants.

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