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CONGEN (CONformation GENerator) is a program performing conformational searches on segments of proteins. It is most suited to problems where one needs to construct underdetermined loops or segments in a known structure, i.e. homology modeling. The program is a modification of CHARMM version 16, and has most of the capabilities of that version of CHARMM. Good references for CONGEN are R. E. Bruccoleri, E. Haber, J. Novotny, "Structure of Antibody Hypervariable Loops Reproduced by a Conformational Search Algorithm", Nature 335, 564-568 (1988); Nature 336, 1266 (1988); R. Bruccoleri and M. Karplus. Biopolymers 26, 137-168 (1987); and B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, David J. States, S. Swaminathan, and Martin Karplus. J. Comput. Chem. 4, 187-217 (1983).
This documentation can be easily perused on-line using the INFO facility under GNU Emacs. INFO provides a text oriented hypertext system where one can navigate throughout the documentation either by the hierarchy of information (chapters, sections, subsections, etc.) or by the cross references.
CONGEN is an non-interactive program. You specify commands in a command file, and they are executed by the program. Error messages and essential results are written to a log file, and other information can be written to files of your own choosing. Commands to CONGEN are generally written in free field format; exceptions are noted in the appropriate manual pages. CONGEN can generate graphics for both non-interactive and interactive use.
Despite the complexities in CONGEN's implementation, CONGEN is designed to be portable. At present, the code has been ported to VAXen running VMS, Silicon Graphics Iris 4D's, Convex C2's, and the Cray YMP.(1) There are a small number of machine dependent features which must be accommodated when porting. In particular, the program is written using both C and FLECS (a Fortran preprocessor), and the interface between languages requires the use of a special program, wrapgen, see section WRAPGEN -- The Wrapper Generator.
CONGEN is provided free of charge. It is my intention that the program be used as widely as possible so that all scientists can benefit from the work that many people have put into it. I do not believe that anyone should reinvent the wheel. However, since CONGEN was written at various institutions with different distribution policies, the program is licensed so that the requests of the sponsoring institutions will be satisfied. I urge all users of CONGEN to honor the license agreement, and if there are any questions or problems, please contact me. I will make every effort to resolve any difficulties.
Although I try to keep CONGEN bug free, it is not. Don't trust the program too much. If you don't understand what it is doing from this manual or its operation, read the source code and run the program with a debugger. The source code and all of the tools necessary to build CONGEN are provided to help you understand it. I especially welcome comments from those who explore its internals.
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