1obminimize(1) User's Reference Manual obminimize(1)
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4 obminimize — optimize the geometry, minimize the energy for a molecule
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7 obminimize [OPTIONS] filename
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10 The obminimize tool can be used to minimize the energy for molecules
11 inside (multi-)molecule files (e.g., MOL2, etc.)
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14 If no filename is given, obminimize will give all options including the
15 available forcefields.
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17 -n steps
18 Specify the maximum number of steps (default=2500)
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20 -cg Use conjugate gradients algorithm (default)
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22 -sd Use steepest descent algorithm
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24 -c criteria
25 Set convergence criteria (default=1e-6)
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27 -ff forcefield
28 Select the forcefield
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31 View the possible options, including available forcefields:
32 obminimize
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34 Minimize the energy for the molecule(s) in file test.mol2:
35 obminimize test.mol2
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37 Minimize the energy for the molecule(s) in file test.mol2 using the Ghem‐
38 ical forcefield:
39 obminimize -ff Ghemical test.mol2
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41 Minimize the energy for the molecule(s) in file test.mol2 by taking at
42 most 300 geometry optimization steps
43 obminimize -n 300 test.mol2
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45 Minimize the energy for the molecule(s) in file test.mol2 using the
46 steepest descent algorithm and convergence criteria 1e-5:
47 obminimize -sd -c 1e-5 test.mol2
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50 babel(1), obenergy(1), obrotamer(1).
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52 The web pages for Open Babel can be found at: <http://openbabel.org/>
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54 The web pages for Open Babel Molecular Mechanics can be found at:
55 <http://openbabel.org/wiki/Molecular_mechanics>
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58 The minimize program was contributed by Tim Vandermeersch.
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60 Open Babel is developed by a cast of many, including currrent maintainers
61 Geoff Hutchison, Chris Morley, Michael Banck, and innumerable others who
62 have contributed fixes and additions. For more contributors to Open
63 Babel, see <http://openbabel.org/wiki/THANKS>
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66 Copyright (C) 2007 by Tim Vandermeersch.
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68 This program is free software; you can redistribute it and/or modify it
69 under the terms of the GNU General Public License as published by the
70 Free Software Foundation version 2 of the License.
71
72 This program is distributed in the hope that it will be useful, but
73 WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABIL‐
74 ITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
75 License for more details.
76
77Open Babel 2.2 July 4, 2008 Open Babel 2.2