AMBER Archive (2006)

Subject: Re: AMBER: PARAMETERISATION PROBLEM

From: David A. Case (case_at_scripps.edu)
Date: Wed Sep 06 2006 - 10:20:43 CDT

On Wed, Sep 06, 2006, Claire Zerafa wrote:
>
> octane2 4% $AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
> -I: Adding /usr/local/amber8/dat/leap/prep to search path.
> -I: Adding /usr/local/amber8/dat/leap/lib to search path.
> -I: Adding /usr/local/amber8/dat/leap/parm to search path.
> -I: Adding /usr/local/amber8/dat/leap/cmd to search path.
> -s: Ignoring startup file: leaprc
> -f: Source /usr/local/amber8/dat/leap/cmd/leaprc.ff99.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [atom.c], line 444
> !FATAL: Message: bondAtomProblem found
> !
> !ABORTING.
> octane2 5%

>From this message it appears that LEaP is crashing just on reading the
standard leaprc files, i.e. that the problem has nothing to do with your
input at all. Does tleap pass the test cases? What flags did you use with
configure? (In particular, it is probably safest to have the -n32 flag turned
on when compiling tleap, assuming that "octane2" is an SGI machine.)

If you actually get to the stage of reading your own files, please note that
all atoms within a resiude must have unique names. Your files violate this
rule. LEaP is not all that good at providing error messages when this
happens.

...regards...dac

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