AMBER Archive (2008)

Subject: AMBER: AmberTools on OS X fails tests

From: Hans Martin Senn (senn_at_chem.gla.ac.uk)
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

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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