This is the documentation for Congen, a conformational search program.
Congen is derived from CHARMM version 16, B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, David J. States, S. Swaminathan, and Martin Karplus. J. Comput. Chem. 4, 187-217 (1983).
If you use CONGEN for research which is published, please cite the following papers:
If you use CONGEN's molecular mechanics features like minimization and dynamics, please cite the reference above for CHARMM as well.
Copyright (C) 1987-1988 Robert E. Bruccoleri
Copyright (C) 1990-1997 Bristol-Myers Squibb Company
This software and related documentation is being provided by the copyright holders under the following license. By obtaining, using and/or copying this software, you agree that you have read, understood, and will comply with the following terms and conditions:
Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice and this permission notice and warranty disclaimer appear in all copies.
ROBERT E. BRUCCOLERI AND BRISTOL-MYERS SQUIBB COMPANY DISCLAIMS, AND THE USER WAIVES, ALL REPRESENTATIONS AND WARRANTIES, EXPRESS OR IMPLIED, WITH REGARD TO THIS SOFTWARE AND ITS RELATED DOCUMENTATION, INCLUDING WITHOUT LIMITATION ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR USE OR PURPOSE. ROBERT E. BRUCCOLERI AND BRISTOL-MYERS SQUIBB COMPANY MAKES NO REPRESENTATION OR WARRANTY, EXPRESS OR IMPLIED, AS TO WHETHER THE USE OF THIS SOFTWARE AND ITS RELATED DOCUMENTATION INFRINGES ANY PATENT, COPYRIGHT, OR OTHER INTELLECTUAL PROPERTY RIGHT OF ANY OTHER PARTY. IN NO EVENT SHALL ROBERT E. BRUCCOLERI OR BRISTOL-MYERS SQUIBB COMPANY BE LIABLE FOR ANY SPECIAL, DIRECT, INDIRECT, INCIDENTAL, PUNITIVE, OR CONSEQUENTIAL DAMAGES, OR ANY OTHER DAMAGES OF ANY NATURE WHATSOEVER, THAT MAY BE INCURRED BY THE USER OR ANY OTHER PARTY ARISING OUT OF OR IN CONNECTION WITH ANY USE OR PERFORMANCE OF THIS SOFTWARE OR ANY USE OF ANY DATA OR RESULTS GENERATED BY THE SOFTWARE, INCLUDING WITHOUT LIMITATION LOSS OF DATA AND LOST PROFITS OR REVENUES, WHETHER OR NOT DR. BRUCCOLERI AND BRISTOL-MYERS SQUIBB COMPANY HAVE BEEN ADVISED OF THE POSSIBILITY OF DAMAGES, AND USER HEREBY WAIVES, RELEASES, AND FOREVER DISCLAIMS ALL DAMAGES, CLAIMS, AND CAUSES OF ACTION IT MAY HAVE AGAINST DR. BRUCCOLERI AND BRISTOL-MYERS SQUIBB COMPANY WITH RESPECT TO ANY LOSSES, DAMAGES, COSTS, EXPENSES, AND LIABILITIES OF ANY NATURE THAT MAY BE INCURRED BY IT ARISING OUT OF OR IN CONNECTION WITH USER'S USE OF THE SOFTWARE AND ITS RELATED DOCUMENTATION. USER SHALL BE SOLELY RESPONSIBLE FOR ALL LOSSES, DAMAGES, COSTS, EXPENSES, AND LIABILITIES OF ANY NATURE INCURRED BY USER RESULTING FROM OR IN CONNECTION WITH USER'S USE OF THE SOFTWARE AND ITS RELATED DOCUMENTATION. THE USER UNDERSTANDS AND ACCEPTS THE ABOVE LIMITATIONS ON DAMAGES AND REMEDIES AS A CONDITION OF OBTAINING USE OF THE SOFTWARE AND RELATED DOCUMENTATION WITHOUT CHARGE.
CONGEN is a trademark of Robert E. Bruccoleri.
Congen contains software from the University of California. Any such code is
Copyright (C) 1991, 1993
The Regents of the University of California. All rights reserved.
Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
This product includes software developed by the University of California, Berkeley and its contributors.
THIS SOFTWARE IS PROVIDED BY THE REGENTS 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 REGENTS 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.
There were many contributors in writing the CONGEN documentation. Bernie Brooks wrote the sections on Vibrational Analysis, Images, and Coordinate Manipulations. Dave States wrote the sections on the Non-bonded Interactions and Parameter File Development. S. Swaminathan wrote the section on Correlation Functions. I also thank Donna Bassolino for reviewing the entire document and for contributing the code for NMR constraints and all hydrogen topology file searching. Susan Cottingham worked on improvements to the coordinate I/O code, specifically on the Brookhaven Protein Data Bank section. A special thanks is extended to Drs. Juan Luis Pascual-Ahuir, Estanislao Silla and Inaki Tunon for making the GEPOL algorithms available for use within CONGEN.
Besides the direct contributors, CONGEN has had many supporters over the years. Dr. Edgar Haber provided the research environment where most of the work was done. His interest in macromolecular structure was essential. When support was difficult to obtain, Dr. Haber was always there. Dr. Jiri Novotny is my closest scientific colleague, and together, we have applied CONGEN to many different modeling problems. Many of the program's capabilities resulted from questions he wanted to answer. Jiri has bestowed me with his considerable knowledge about protein structure as well as his experience as a scientist. Professor Guy Montelione was a key collaborator in the development of the NMR constraint code, and Dr. Keith Constantine conceived of the ensemble averaging concept. Professor Martin Karplus was my Ph.D. advisor, and the laboratory that he established was the womb where CONGEN was created. I thank Professor Karplus, Mick Savage from Molecular Solutions Inc., Joyce Brinton and Bristol-Myers Squibb for permitting me to make CONGEN freely available and redistributable. Special gratitude goes to John Mesrobian, Annette Tobia, and Ed Penick for all their legal help over the years with CONGEN. The command processing language was inspired by the GRIPHOS package developed by Professor Jack Heller at the State University of New York at Stony Brook. Finally, Richard M. Stallman gave me the inspiration that CONGEN should be free.
This manual was formatted using the Texinfo macros running with TeX.
Go to the first, previous, next, last section, table of contents.