AMBER Archive (2009)

Subject: Re: [AMBER] failure to run antechamber with amber 10

From: David A. Case (
Date: Thu Jan 29 2009 - 16:45:53 CST

On Thu, Jan 29, 2009, Francesco Pietra wrote:

> with amber10/ambertools 1.2 i was unable to run antechamber, as
> indicated below (i can't remember if this is the 1st time i am dealing
> with antechamber in ambertools 1.2)
> $AMBERHOME/exe/antechamber -i myfile.pdb -fi pdb -o myfile.prepin -fo
> prepi -c bcc -s 2
> returned the error:
> Error: cannot run "/usr/local/amber10/bin/bondtype -j full -i
> judgebondtype() of antechamber.c properly, exit
> Running: /usr/local/amber10/bin/bondtype -j full -i

Is this the *only* output/error? Usually, other things are printed
which suggest the origin of the problem.

I'm assuming that the antechamber test cases all pass. That strongly
implies that there is something about myfile.pdb that is leading to
problems that are not be caught by the test suite. But since we don't
have access to your particular input file, it's unclear what sort of
help you are really expecting.

Of course, having an actual example of something that (seems to) work in
Amber 9 but fails in Amber10 (i.e. a regression) would be of interest.

[You're pretty experienced with both Amber and this mailing list; you
should already appreciate the points raised above.]


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