Chem3D Users Manual - CambridgeSoft

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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. 294• MOPAC CambridgeSoft Adding Parameters to MOPAC
Index Symbols (-CHR-) bending force parameters 282 .3dm file format 121 .alc file format 118, 121 .avi file formats 121 .bmp file format 119 .cc1 file format 118, 121 .cc2 file format 118, 121 .cdx file format 118 .con file format 122 .ct file format 118, 122 .cub file format 122 .dat file format 123 .emf file format 119 .eps file format 120 .fch file format 122 .gif file format 121 .gjc file format 118, 122 .gjf file format 122, 203 .gjt file format 203 .gpt file format 126 .int file format 118, 123 .jdf file format 126, 202 .jdf Format 202 .jdt file format 126, 202 .jdt Format 202 .mcm file format 118, 123 .ml2 file format 126 .mol file format 118, 124 .mop file format 118, 124 .mpc file format 124 .msm file format 118, 124 .pdb file format 118, 126 .png file format 121 .rdl file format 118, 126 .sm2 file format 118, 126 .smd file format 118, 126 .sml file format 118, 126 .xyz file format 126 .zmt file format 124 Numerics 1/2 electron approximation 147, 166 2D programs, using with Chem3D 75 2D to 3D conversion 239 3D enhancement depth fading 60 hardware 62 red-blue 59 stereo pairs 61 3RINGANG.TBL see Angle bending table 4-Membered Ring Torsionals 271 4RINGANG.TBL see Angle bending table A Ab initio methods speed 130 uses 131 vs. semi-empirical methods 146 Activating the select tool 38 Actual field editing 107 Actual field measurements 29 ACX information, finding 225 ACX, number search 226 ACX, structure search 225 Adding calculations to an existing worksheet 220 formal charges 77 Chem3D Chem3D 9.0.1 • i
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ChemOffice.Com ® ChemOffice ® Che
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License Information ChemOffice, Che
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· Licensed users of ChemOffice Ent
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computer, except as provided below.
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Q: IS IT OK TO COPY MY COLLEAGUE’
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A Guide to CambridgeSoft Manuals An
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Administrator Setting Molecular Sur
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Administrator Methods Available in
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Administrator Defining Atom Types.
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Administrator • CambridgeSoft
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Administrator provides a balance be
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Administrator the activation each t
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Administrator The following table d
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Administrator • Stereo Pairs—A
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Administrator • Bond Angles—Dis
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Administrator The Building Toolbar
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Administrator The Calculation Toolb
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Administrator 1. Right-click in the
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Administrator • In the Model Sett
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Administrator modes and color setti
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Administrator 30 •Chem3D Basics C
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Administrator 2. Click the ChemDraw
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3. Move the pointer over the C-C bo
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Administrator Add serial numbers an
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Administrator 5. Press the Enter ke
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. Administrator b. From the Structu
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Administrator In the Measurements t
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A molecule of Epinephrine appears.
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Administrator Tutorial 7: Docking M
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Administrator To save the iteration
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The allyl radical, CH 2 =CHCH 2·,
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Administrator Determine the raw spi
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Administrator atoms are relatively
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To change the structural display ty
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Administrator When sizing by partia
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Administrator Depth Fading3D enhanc
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• Select Parallel to rotate the r
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Administrator • From the Computat
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Administrator Surface Type Solid De
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Administrator 2. Adjust the slider
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Administrator Density surface is ca
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Administrator 72 •Displaying Mode
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Administrator The following table d
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Administrator When Correct Atom Typ
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Administrator To use the same text
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Administrator Example 2. Building a
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Administrator copied into blank tab
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Administrator 3. Type the atom type
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Administrator Clean Up Structure or
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Setting Serial Numbers this step, y
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Administrator Refining a Model Afte
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Administrator Selecting Multiple At
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Administrator New in Chem3D version
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Administrator Dragging moves atoms
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Administrator 3. Hold down the Shif
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To position a plane in your model p
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Administrator • Second Positioned
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Administrator For example, consider
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Administrator If you want to displa
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Administrator Example: To examine t
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Administrator Chem3D provides two o
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Administrator change a property. By
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Administrator To add to a group: 1.
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To stop spinning: • On the Movie
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Administrator If you want to … Th
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Administrator EPS The PostScript fi
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If you want the file to … Then cl
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Molecular Design Limited MolFile (.
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Administrator 7. Leave the last lin
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Administrator 128•Printing and Ex
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Administrator • Semiempirical Ext
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Method Type Advantages Disadvantage
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Administrator • A single point ca
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Administrator • Molecular mechani
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Administrator constant), while θ 0
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Administrator The van der Waals int
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Administrator 6. The modified value
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the same wave function and a consta
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Administrator A variety of other ba
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Administrator Molecular wave functi
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Administrator activation barriers.
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3. From the Calculations menu, poin
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minimizing a second model, the mini
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Administrator move to lower the ene
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. Administrator Molecular Dynamics
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Administrator If you want to … Th
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Administrator The Compute Propertie
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Administrator To run a previously c
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Administrator The procedures assume
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Administrator improvements in each
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Administrator • Overall errors in
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Administrator The following table c
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Administrator TRIPLET QUARTET QUINT
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Administrator Chemical symbol ++ ba
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Administrator 4. Click Run. A new m
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Administrator Minimizing Energy Min
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Administrator criteria, to optimize
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Administrator 6. Hold down the S ke
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Administrator Dipole Moment The dip
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Administrator Molecular Surfaces Mo
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The following table contains the ke
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Administrator 3. Click in the model
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Keyword Description 7. On the Prope
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Administrator Hyperfine Coupling Co
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Administrator 198•MOPAC Computati
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Administrator If you want to … re
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Administrator In the Results In tex
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Administrator Repeating a Gaussian
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Property Description Property Descr
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Property Description Error Message
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Administrator Property Electronic E
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Administrator To specify the calcul
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Administrator 3. Click Open. The ap
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Administrator • Server—limits t
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Administrator To perform property c
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The Step 4 of 4 dialog box appears.
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Administrator • From the ChemOffi
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Administrator Accessing the Online
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Administrator To find a structure t
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Administrator 228• Accessing the
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Administrator Performance Below are
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Administrator Defining Substructure
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Administrator If an atom can be ass
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Key Drag Shift+Drag Administrator Q
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Administrator 238• Keyboard Modif
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Administrator Example 3 In Example
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Administrator 14 13 H 2.197 -0.8229
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Page 272 and 273: Administrator CONECT 4 2 9 10 11 CO
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Page 284 and 285: Parameter Table Use Parameter Table
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DISCOVERY • Integrated with Regis
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DISCOVERY • Reagent lists can be
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DISCOVERY •Effectively manages da
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DISCOVERY • Catalog driven data m
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DATABASES • Fully structure-searc
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DATABASES • Encyclopedic referenc
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DATABASES • Extensive collection
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SERVICES · Business Case Developme
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CS ChemOffice ® Desktop to Enterpr
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Chem3D Users Manual - CambridgeSoft

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