Hi,
On Wed, Nov 25, 2009 at 04:59:37PM -0500, Ben Roberts wrote:
> All:
>
> It seems that something is going very wrong inside bondtype.c on
> chemokine.
>
> 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)
> gracefully.
>
> 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
Thanks for your work.
Whats the web server address ?
scott
> 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.
>
> Ben
>
> 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 \
> > -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> >
> > 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
> > > -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
> > > 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 - 14:30:04 PST
