AMBER Archive (2008)

Subject: AMBER: AmberTools on OS X fails tests

From: Hans Martin Senn (
Date: Thu May 08 2008 - 13:59:12 CDT

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

< 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 && ./ diffing with tp.mol2 possible FAILURE: check tp.mol2.dif ============================================================== cd antechamber/ash && ./Run.ash diffing with ash.mol2 possible FAILURE: check ash.mol2.dif ============================================================== cd antechamber/sustiva && ./Run.sustiva diffing with sustiva.mol2 possible FAILURE: check sustiva.mol2.dif ============================================================== cd antechamber/fluorescein && ./Run.fluorescein diffing 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 with box.out possible FAILURE: check box.out.dif ============================================================== cd solvate; ./Run.solvatebox long test, wait patiently... diffing with hpvbox.pdb possible FAILURE: check hpvbox.pdb.dif ============================================================== cd solvate; ./Run.solvatecap diffing with hpvcap.pdb possible FAILURE: check hpvcap.pdb.dif ============================================================== cd solvate; ./Run.solvateoct long test, wait patiently... diffing with hpvoct.pdb possible FAILURE: check hpvoct.pdb.dif ============================================================== cd solvate; ./Run.solvateshell long test, wait patiently... diffing with hpvshell.pdb possible FAILURE: check hpvshell.pdb.dif ============================================================== cd amoeba; ./Run.amoeba_sol diffing with hpv.prmtop possible FAILURE: check hpv.prmtop.dif ============================================================== cd addions; ./Run.addions diffing with glu.mol2 possible FAILURE: check glu.mol2.dif

Cheers Hans

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