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Administrator Adding Parameters to MOPAC Parameters are in constant development for use with PM3 and AM1 potential functions. If you find that the standard set of parameters that comes with CS MOPAC does not cover an element that you need, for example Cu, you can search the literature for the necessary parameter and add it at run time when performing a MOPAC job. This flexibility greatly enhances the usefulness of MOPAC. You can add parameters at run time using the keyword EXTERNAL=name, where name is the name of the file (and its full path) containing the additional parameters. A description of the required format for this file can be found in Figure 3.4, page 43 of the MOPAC 2000 V.1.3 manual included on the CD-ROM. 676• MOPAC <strong>CambridgeSoft</strong> Adding Parameters to MOPAC
Appendix K: Structural Query Features Overview To perform a substructure search in ChemFinder, you must first draw the query structure itself. Query structures can be drawn in many different programs, but we recommend using ChemDraw, and this Appendix is focused on using ChemDraw to draw query structures. For more information about the structure drawing and query capabilities of ChemDraw, please consult the ChemDraw User’s Guide. ChemFinder does its best to follow your instructions even if those instructions are contradictory. For example, you can create a query such as the following: Atoms Atom types specified in the query must match atoms at corresponding positions in the target. Hydrogen is an exception—see “Substituents” on page 678. Bonds All bonds explicitly drawn in the query must match in the target. For certain caveats, see “Stereochemistry” on page 679 and “Normalization” on page 681. ChemFinder recognizes the following standard bond types: Bond Type Description Chn This bond must not be in a ring. Single target must have single bond here That bond is already in a ring, so ChemFinder returns no hits for this query. General Properties ChemFinder allows the following general properties to be assigned to a query: Dashed Hashed Thick same as Single same as Single same as Single • Atom • Bond • Substituents • Charges and radicals • Isotopes • Stereochemistry • Normalization Wedged Hashed specifies stereochemistry down from the point end to the wide end Wedged specifies stereochemistry up from the point end to the wide end Appendices <strong>ChemOffice</strong> 2005/Appendix Structural Query Features • 677 General Properties
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Chapter 31: Changes and Audit Trail
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Administrator Tutorial 7: Docking M
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CAMBRIDGESOFT ChemOffice Desktop to
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