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Legal Notices Schrödinger Software Modules Legal Notices Schrödinger Software Modules Copyright © Schrödinger, LLC. All rights reserved. BioLuminate, Canvas, CombiGlide, ConfGen, Epik, Glide, Impact, Jaguar, Liaison, LigPrep, Maestro, Phase, Prime, PrimeX, QikProp, QikFit, QikSim, QSite, SiteMap, Strike and WaterMap are trademarks of Schrödinger, LLC. Schrödinger and MacroModel are registered trademarks of Schrödinger, LLC. MCPRO is a trademark of William L. Jorgensen. Desmond is a trademark of D.E. Shaw Research. Desmond is used with the permission of D. E. Shaw Research. All rights reserved. Third-Party Software, Libraries and Utilities The following required legal notices pertain to certain third party software, libraries and utilities distributed with one or more of Schrödinger’s software modules. The legal notices that apply to you will depend on your particular installation and use of the Schrödinger software modules. 7zsd.sfx AMBER Force Field Parameters APBS (Adaptive Poisson-Boltzmann Solver) BioPython BLT Toolkit C and C++ Libraries for Parsing PDB Records CHARMM Force Field Parameters ClustalW ConfigObj Desmond Molecular Dynamics System Eclipse epydoc FFmpeg The FreeType Project FTGL Glut GNU General Public License v 2.1 GNU Lesser General Public License v 2.1 HMMER Jmol libpng MatPlotlib MOPAC NCSA HDF5 (Hierarchical Data Format 5) Software Library and Utilities NetworkX Numeric NumPy Open MPI The Open Source ReportLab Library OpenSSL PFAM Pfam-A.seed.gz Piper PMW PROPKA Pychecker Python Python Imaging Library pytz PyYAML SciPy SDG Technology setuptools simplejson stdint.h UnxUtils virtualenv Visualization Toolkit (VTK) Water Models Water Site Analysis Software zlib.h 7zsd.sfx Author: Oleg Scherbakov. Used only for inserting extraction scenarios in SFX archives. Distributed by the GNU Lesser General Public License v 2.1 . AMBER Force Field Parameters ==> amber03 "info" : ["Duan et al. (2003), J. Comp. Chem. 24, 1999-2012", "Parameters converted from those at http://amber.scripps.edu/amber9.ffparms.tar.gz", "Bugfix from http://amber.scripps.edu/bugfixes/9.0/bugfix.5 applied to correct torsion assignments" ] ==> amber94 "info" : ["Cornell et al. (1995), JACS 117, 5179-5197", "Parameters converted from those at http://amber.scripps.edu/amber9.ffparms.tar.gz"] ==> amber96 "info" : ["Kollman (1996), Acc. Chem. Res. 29, 461-469", "Parameters converted from those at http://amber.scripps.edu/amber9.ffparms.tar.gz"] ==> amber99 "info" : ["Wang et al. (2000), J. Comp. Chem. 21, 1049-1074", "Parameters converted from those at http://amber.scripps.edu/amber9.ffparms.tar.gz"] ==> amber99SB "info" : ["Wang et al. (2000), J. Comp. Chem. 21, 1049-1074", "Hornak et al. (2006), Proteins: Structure, Function and Genetics, 3:712-725.", "Parameters converted from those at http://amber.scripps.edu/amber9.ffparms.tar.gz"] APBS (Adaptive Poisson-Boltzmann Solver) Nathan A. Baker ([email protected] or [email protected]) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2011 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: • Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. • Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. • Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. Distributed by the GNU Lesser General Public License v 2.1. The modified libraries are available at the following location: !p://!p.schrodinger.com/support/gpl_lgpl/apbs-contrib.tgz BioPython For copyright notices related to BioPython see individual source files. Biopython License Agreement Permission to use, copy, modify, and distribute this software and its documentation with or without modifications and for any purpose and without fee is hereby granted, provided that any copyright notices appear in all copies and that both those copyright notices and this permission notice appear in supporting documentation, and that the names of the contributors or copyright holders not be used in advertising or publicity pertaining to distribution of the software without specific prior permission. THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE. BLT Toolkit Copyright 1998-2004 George A Howlett. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. C and C++ Libraries for Parsing PDB Records © 1989 The Regents of the University of California. All rights reserved. Redistribution and use in source and binary forms are permitted provided that the above copyright notice and this paragraph are duplicated in all such forms and that any documentation, advertising materials, and other materials related to such distribution and use acknowledge that the software was developed by the University of California, San Francisco. The name of the University may not be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED AS IS AND WITHOUT ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE. CHARMM Force Field Parameters ==> charmm22 "info" : [ "MacKerell et al. (1998), J. Phys. Chem. B. 102, 3586-3616 (proteins)", "Beglov et al. (1994), J. Chem. Phys. 100, 9050-9063 (ions)", "parameters generated from http://www.pharmacy.umaryland.edu/faculty/amackere/param/toppar/toppar_c31b1.tar.gz" ==> charmm27 "info" : [ "MacKerell et al. (2004), J. Comp. Chem. 25, 1400-1415 (protein cmap)", "MacKerell et al. (1998), J. Phys. Chem. B. 102, 3586-3616 (proteins)", "Beglov et al. (1994), J. Chem. Phys. 100, 9050-9063 (ions)", "parameters generated from http://www.pharmacy.umaryland.edu/faculty/amackere/param/toppar/toppar_c31b1.tar.gz" ClustalW v. 2.0.11 Copyright November 2007. Authors: Des Higgins, Julie Thompson and Tony Gibson. The binaries and source code are made available and can be distributed subject to the following conditions: - Users are free to redistribute ClustalW or ClustalX in it's unmodified form as long as it is not for commercial gain. - Anyone wishing to redistribute Clustal commercially should contact Toby Gibson at [email protected] - If users make changes/have ideas that they believe would be useful to the broader research community they can send their suggestions to the clustal development team at [email protected] where they will be considered for inclusion in future releases. ConfigObj ConfigObj ver. 4 Copyright (c) 2004 - 2006, Michael Foord & Nicola Larosa All rights reserved. Redistribution and use in source and binary forms, with or without modification,
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