Re: [AMBER-Developers] test request for ambertools and Snow Leopard 64 bits kernel

From: Ben Roberts <>
Date: Wed, 25 Nov 2009 16:59:37 -0500


It seems that something is going very wrong inside bondtype.c on

In my case, the fatal error is triggered because there exists a bond for
which jflag is set to 1 on Snow Leopard, compared to -1 for Linux. This
causes the code to travel down a different path, where it checks for the
frozen atom type, discovers that it's 0, and exits (relatively)

However, that's not the only discrepancy between Linux and Snow Leopard.
Many of the entries for parts of BOND data structures (type, type2,
jflag, etc.) are different. Sometimes, on Linux, the type entry for a
certain bond will contain a large negative number (in the millions or
higher), while on Snow Leopard the type entry for the same bond will be
0. Other times the difference is more subtle (e.g., -2 instead of 0, or
the flag case above).

I have put a bunch of files up on a web server, rather than trying to
send them to the list, since some of them are large. I hope this is OK.
If it's a problem, let me know and I can take them down.

* bondtype.c - modified by turning debug on at the top of the file, and
added a bunch of print statements.

* 1b2t.csh - a modified version of Run.1b2t, but things are appended to
"antechamber.out" rather than overwriting it.

* and two text files (originally called antechamber.out, and produced by
1b2t.csh) - one generated on a Linux box, and the other on Snow Leopard.
Which is which should be obvious from the names of the files.

I hope that helps people figure out what's going on here, and that it's
not another NAB-like problem. Those who are working on this, let me know
if you would like more information or a trial run of something.


On Tue, 2009-11-24 at 11:36 -0500, Volodymyr Babin wrote:
> Hi everyone,
> I don't have the OS around unfortunately to try it myself.
> You could try to run [change -pf yes to -pf no first]
> /Applications/Amber11/intel-mkl/bin/bondtype -j full \
> manually and examine the output if it is wrong indeed (to rule out
> some parsing errors). You could then try to nail it down further
> by injecting 'printf()' statements around. Alternatively, I could
> take a look if someone could give me a (temporary) shell at a leopard.
> Best,
> Volodymyr
> On Tue, November 24, 2009 11:27, Ben Roberts wrote:
> > Hi Scott,
> >
> > Last I knew, this problem still exists. It seems bondtype() was
> > returning the wrong values for certain things.
> >
> > Specifically:
> >
> > <snip>
> >
> > ---Judge bond type for Residue 12 with ID of 11 and Name of THR ---
> >
> > The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8
> > (aromatic double)
> > Error: cannot run "/Applications/Amber11/intel-mkl/bin/bondtype -j full
> > judgebondtype() of antechamber.c properly, exit
> >
> > Interestingly enough, it grumbles at a different point to Alan's
> > original bug report.
> >
> > I'll see what I can find. Is there any indication as to what,
> > technically speaking, is causing the problem?
> >
> > Ben
> >
> > Scott Brozell wrote:
> >> Hi,
> >>
> >> What is the status of the antechamber tests on Uncia uncia ?
> >> In particular, does the chemokine problem at the tail below still exist
> >> ?
> >>
> >> thanks,
> >> Scott

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Received on Wed Nov 25 2009 - 14:30:02 PST
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