mmtk1.1b1 on DEC AlphaStation

James A. Lupo lupoja@feynman.ml.wpafb.af.mil
Tue, 14 Jul 1998 14:23:20 -0400


I've installed Python-1.5.1 on a DEC AlphaStation 250 4/266 running
OSF1/4.0a.  I used:

	    gcc-2.8.1	    
	    libz-1.1.3
	    Tcl/Tk-8.0
	    Tix4.1.8.0
	    BLT2.3
	    netcdf-3.4

All self-tests completed okay on these packages, and the python "make
test" ran to completion with a minor error from the zlib module.

MMTK installed okay, but NONE of the sample scripts work, nor does the
"A simple example" in overview.html (once the bugs/typos are fixed!).

I've attached the outputs below my signature block.  By manually
typing in the scripts which failed due to Floating Point Exceptions, I
found them caused by calls to minimizer() or integrator().  dlpoly.py
failed with an "energy evaluator defined only for universes" message.
Neither protein_analyze.py nor I could find 4q21.pdb.
protein_construction.py ran into an unknown atom type.

My questions to the group are:

1.  Given that the last three examples failed due to apparently
incorrect coding or data, can anyone verify that the remaining
examples do indeed work?

2.  Has anyone successfully set up MMTK on an AlphaStation?

-- 
Jim

    ------------------- Optional Methods -----------------------
     HARDCOPY           |                 ELECTRONIC
ATTN: DR JAMES A LUPO   | COMM:  (937) 255-6671, Ext 3160 (voice/message)
AFRL/MLPJ BLDG 651      | FAX:   (937) 255-1128
3005 P ST STE 1         | DSN:   CONUS 785-6671, Ext 3160 (voice/message)
WPAFB OH 45433-7702     | EMAIL: lupoja@feynman.ml.wpafb.af.mil (134.131.35.31)

##############################  ERROR OUTPUT  ##############################

constrained_modes.py:

Floating exception (core dumped) - caused by minimizer()


dynamics.py:

Temperature:  50.7326259183
Momentum:  [-14.050640665, 7.39245674755, 0.358061046558]
Angular momentum:  [1.03316324648, -1.09062408269, 0.556528231758]
Floating exception (core dumped) - Caused by integrator()


solvent.py:

Floating exception (core dumped) - Caused by minimizer()


modes.py:

Floating exception (core dumped) - Caused by minimizer()


dlpoly.py:

Traceback (innermost last):
  File "dlpoly.py", line 10, in ?
    DLPOLY(hemo, AmberForceField(), 'insulin')
  File "/usr/local/lib/mmtk-1.1b1/DLPOLY.py", line 55, in __init__
    EnergyEvaluator.__init__(self, universe, force_field)
  File "/usr/local/lib/mmtk-1.1b1/ForceField.py", line 196, in __init__
    raise TypeError, "energy evaluator defined only for universes"
TypeError: energy evaluator defined only for universes


protein_analysis.py:  Unknown PDB file

Traceback (innermost last):
  File "protein_analysis.py", line 11, in ?
    sequences_1 = PDBFile('4q21.pdb').readSequenceWithConfiguration()
  File "/usr/local/lib/mmtk-1.1b1/ConfigIO.py", line 27, in __init__
    raise IOError, 'File ' + filename + ' not found'
IOError: File /usr/local/lib/mmtk-1.1b1/PDB/4q21.pdb not found


protein_construction.py:  Unknown Atom type

Traceback (innermost last):
  File "protein_construction.py", line 38, in ?
    chains.append(PeptideChain(chain, hydrogens='none'))
  File "/usr/local/lib/mmtk-1.1b1/Protein.py", line 150, in __init__
    ConfigIO.PDBConfiguration(conf).applyTo(self, 1)
  File "/usr/local/lib/mmtk-1.1b1/ConfigIO.py", line 71, in applyTo
    self._applyTo(object, initial, self._conf)
  File "/usr/local/lib/mmtk-1.1b1/ConfigIO.py", line 105, in _applyTo
    total = total - self._applyResidue(conf[i], map[0], g, alt)
  File "/usr/local/lib/mmtk-1.1b1/ConfigIO.py", line 132, in _applyResidue
    raise IOError, 'Atom ' + atom.name + ' of PDB residue ' + \
IOError: Atom 2HT of PDB residue GLY not found in residue Gly of object .Gly1


####################  Corrected "A Simple Example"  ####################

( This also fails with a Floating Point Exception upon call to integrator() )

from mmtk import *
universe = InfiniteUniverse(AmberForceField())
universe.molecule = Molecule('water')
universe.initializeVelocitiesToTemperature(300.*Units.K)
integrator = VelocityVerletIntegrator(universe)
trajectory = Trajectory(universe, "water.nc", "w")
integrator(delta_t = 1.*Units.fs, steps = 50,
           log=(0, None, 5, stdout, ("time","energy")),
           trajectory=(0, None, 1, trajectory, ("time", "energy",
           "temperature", "configuration")))
trajectory.close()


I've installed Python-1.5.1 on a DEC AlphaStation 250 4/266 running
OSF1/4.0a.  I used:

	    gcc-2.8.1	    
	    libz-1.1.3
	    Tcl/Tk-8.0
	    Tix4.1.8.0
	    BLT2.3
	    netcdf-3.4

All self-tests completed okay on these packages, and the python "make
test" ran to completion with a minor error from the zlib module.

MMTK installed okay, but NONE of the sample scripts work, nor does the
"A simple example" in overview.html (once the bugs/typos are fixed!).

I've attached the outputs below my signature block.  By manually
typing in the scripts which failed due to Floating Point Exceptions, I
found them caused by calls to minimizer() or integrator().  dlpoly.py
failed with an "energy evaluator defined only for universes" message.
Neither protein_analyze.py nor I could find 4q21.pdb.
protein_construction.py ran into an unknown atom type.

My questions to the group are:

1.  Given that the last three examples failed due to apparently
incorrect coding or data, can anyone verify that the remaining
examples do indeed work?

2.  Has anyone successfully set up MMTK on an AlphaStation?

-- 
Jim

    ------------------- Optional Methods -----------------------
     HARDCOPY           |                 ELECTRONIC
ATTN: DR JAMES A LUPO   | COMM:  (937) 255-6671, Ext 3160 (voice/message)
AFRL/MLPJ BLDG 651      | FAX:   (937) 255-1128
3005 P ST STE 1         | DSN:   CONUS 785-6671, Ext 3160 (voice/message)
WPAFB OH 45433-7702     | EMAIL: lupoja@feynman.ml.wpafb.af.mil (134.131.35.31)

##############################  ERROR OUTPUT  ##############################

constrained_modes.py:

Floating exception (core dumped) - caused by minimizer()


dynamics.py:

Temperature:  50.7326259183
Momentum:  [-14.050640665, 7.39245674755, 0.358061046558]
Angular momentum:  [1.03316324648, -1.09062408269, 0.556528231758]
Floating exception (core dumped) - Caused by integrator()


solvent.py:

Floating exception (core dumped) - Caused by minimizer()


modes.py:

Floating exception (core dumped) - Caused by minimizer()


dlpoly.py:

Traceback (innermost last):
  File "dlpoly.py", line 10, in ?
    DLPOLY(hemo, AmberForceField(), 'insulin')
  File "/usr/local/lib/mmtk-1.1b1/DLPOLY.py", line 55, in __init__
    EnergyEvaluator.__init__(self, universe, force_field)
  File "/usr/local/lib/mmtk-1.1b1/ForceField.py", line 196, in __init__
    raise TypeError, "energy evaluator defined only for universes"
TypeError: energy evaluator defined only for universes


protein_analysis.py:  Unknown PDB file

Traceback (innermost last):
  File "protein_analysis.py", line 11, in ?
    sequences_1 = PDBFile('4q21.pdb').readSequenceWithConfiguration()
  File "/usr/local/lib/mmtk-1.1b1/ConfigIO.py", line 27, in __init__
    raise IOError, 'File ' + filename + ' not found'
IOError: File /usr/local/lib/mmtk-1.1b1/PDB/4q21.pdb not found


protein_construction.py:  Unknown Atom type

Traceback (innermost last):
  File "protein_construction.py", line 38, in ?
    chains.append(PeptideChain(chain, hydrogens='none'))
  File "/usr/local/lib/mmtk-1.1b1/Protein.py", line 150, in __init__
    ConfigIO.PDBConfiguration(conf).applyTo(self, 1)
  File "/usr/local/lib/mmtk-1.1b1/ConfigIO.py", line 71, in applyTo
    self._applyTo(object, initial, self._conf)
  File "/usr/local/lib/mmtk-1.1b1/ConfigIO.py", line 105, in _applyTo
    total = total - self._applyResidue(conf[i], map[0], g, alt)
  File "/usr/local/lib/mmtk-1.1b1/ConfigIO.py", line 132, in _applyResidue
    raise IOError, 'Atom ' + atom.name + ' of PDB residue ' + \
IOError: Atom 2HT of PDB residue GLY not found in residue Gly of object .Gly1


####################  Corrected "A Simple Example"  ####################

( This also fails with a Floating Point Exception upon call to integrator() )

from mmtk import *
universe = InfiniteUniverse(AmberForceField())
universe.molecule = Molecule('water')
universe.initializeVelocitiesToTemperature(300.*Units.K)
integrator = VelocityVerletIntegrator(universe)
trajectory = Trajectory(universe, "water.nc", "w")
integrator(delta_t = 1.*Units.fs, steps = 50,
           log=(0, None, 5, stdout, ("time","energy")),
           trajectory=(0, None, 1, trajectory, ("time", "energy",
           "temperature", "configuration")))
trajectory.close()