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June 2009 Contents Document Conventions. vii Chapter 1 Introduction. 1 1. 1 The LigPrep Manual. 1 1. The manual is organized as follows Chapter 1 provides an overview of LigPrep and the process it uses to prepare ligands. See the MacroModel Reference Manual for details. In addition the CHIP and CHOP opcodes described below are available only with a LigPrep license. Torsional sampling level to use in bmin. Overrides the -btc option and sets it to .

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