Hi Hans,
I can confirm the Sleap failures are caused by the bug fixes and
is supposed to happen.
Sincerely,
Wei
On May 8, 2008, at 1:59 PM, Hans Martin Senn wrote:
> Dear all
>
> I installed AmberTools on a Mac (Intel/10.4.11). I applied all the
> patches (bug fixes 1-6) and used Apple's gcc and g++ compilers
> (4.0.1) and g77 3.4.3.
> Running the test suite generates the following failures. It would be
> great to hear from other users if they have encountered the same
> problems and from developers if those failures are actually serious.
>
> 1) A too stable minimum. Should I worry?
> =====================================================
> Running test to do simple lmod optimization
>
> 1c1
> < Glob. min. E = -122.793 kcal/mol
> ---
> > Glob. min. E = -144.597 kcal/mol
> FAILED (probably OK if energy is -115 to -125)
>
> 2) A couple of antechamber failures due to (slightly) differing
> charges. Some of these cases also fail on a Linux machine. Reason to
> worry?
> ==============================================================
> cd antechamber/tp && ./Run.tp
> diffing tp.mol2.save with tp.mol2
> possible FAILURE: check tp.mol2.dif
> ==============================================================
> cd antechamber/ash && ./Run.ash
> diffing ash.mol2.save with ash.mol2
> possible FAILURE: check ash.mol2.dif
> ==============================================================
> cd antechamber/sustiva && ./Run.sustiva
> diffing sustiva.mol2.save with sustiva.mol2
> possible FAILURE: check sustiva.mol2.dif
> ==============================================================
> cd antechamber/fluorescein && ./Run.fluorescein
> diffing fluorescein.mol2.save with fluorescein.mol2
> possible FAILURE: check fluorescein.mol2.dif
>
> 3) Sleap problems. If I understand correctly these are all caused by
> the bug fixes applied. Could anybody (the author of the patches?)
> confirm this?
> ==============================================================
> cd prmtop; ./Run.prmtop2
> this is long test, wait paitently.....
> diffing box.out.save with box.out
> possible FAILURE: check box.out.dif
> ==============================================================
> cd solvate; ./Run.solvatebox
> long test, wait patiently...
> diffing hpvbox.pdb.save with hpvbox.pdb
> possible FAILURE: check hpvbox.pdb.dif
> ==============================================================
> cd solvate; ./Run.solvatecap
> diffing hpvcap.pdb.save with hpvcap.pdb
> possible FAILURE: check hpvcap.pdb.dif
> ==============================================================
> cd solvate; ./Run.solvateoct
> long test, wait patiently...
> diffing hpvoct.pdb.save with hpvoct.pdb
> possible FAILURE: check hpvoct.pdb.dif
> ==============================================================
> cd solvate; ./Run.solvateshell
> long test, wait patiently...
> diffing hpvshell.pdb.save with hpvshell.pdb
> possible FAILURE: check hpvshell.pdb.dif
> ==============================================================
> cd amoeba; ./Run.amoeba_sol
> diffing hpv.prmtop.save with hpv.prmtop
> possible FAILURE: check hpv.prmtop.dif
> ==============================================================
> cd addions; ./Run.addions
> diffing glu.mol2.save with glu.mol2
> possible FAILURE: check glu.mol2.dif
>
>
> Cheers
> Hans
>
>
>
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Received on Sun May 11 2008 - 06:07:33 PDT
