| 1 | #!/usr/bin/env python
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| 2 | # minimization.py
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| 3 | #
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| 4 | # Copyright 2007 Frank Eisenmenger, U.H.E. Hansmann,
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| 5 | # Jan H. Meinke, Sandipan Mohanty
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| 6 | #
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| 7 | """Minimize the energy of met-enkaphalin starting from a given structure using
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| 8 | conjugate gradient.
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| 9 | """
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| 10 | # Adds the source directory to Python's search path.
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| 11 | import sys
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| 12 | sys.path.append('../..')
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| 13 | import smmp, universe, protein
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| 14 |
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| 15 | # Initialize the Universe to T=300K with the ECEPP/3 force field, no solvent
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| 16 | # term (st = 0) and the sub directory SMMP/ as library path. Except for the
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| 17 | # solvent term, these are the default values. Alternatively, we could have
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| 18 | # written
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| 19 | # myUniverse = universe.Universe(st=0)
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| 20 | # to get the same result.
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| 21 | myUniverse = universe.Universe(T=300, ff = 'ecepp3', st = 0, libdir ='SMMP/')
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| 22 | # Create a new protein object from the sequence file ../enkefa.seq and
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| 23 | # set the dihedral angles according to the values given in ../enkefa.var.
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| 24 | p = protein.Protein('../enkefa.seq', '../enkefa.var')
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| 25 | # Make myUniverse aware of p.
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| 26 | myUniverse.add(p)
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| 27 | typeOfMinimization = 1
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| 28 | maxNumberOfIterations = 10000
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| 29 | desiredPrecision = 1.0e-9
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| 30 |
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| 31 | smmp.minim(typeOfMinimization, maxNumberOfIterations, desiredPrecision)
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