Chem3D Users Manual - CambridgeSoft

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Administrator repeating jobs 178 RHF 181 running input files 177 server 209 specifying electronic state 172 specifying keywords 170, 181 troubleshooting 176 UHF 181 Move to X-Y plane command 99 to X-Z plane command 99 to Y-Z plane command 99 Movie control panel 116 Movie controller, speed control 116 Movie file format 121 Movie toolbar 21 Movies editing 116 overview 115 Moving atoms 95 models see Translate MOZYME 180 MSI ChemNote file format 124 MSI MolFile 253 Mulliken charges 186 Multiple models 84 N Name field 274 Name=Struct 75 Naming a selection 93 NOMM keyword 172 Non-bonded distances, constraints 142 Non-bonded distances, displaying 106 Non-bonded distances, displaying in tables 107 Non-bonded energy 139 O Odd-electron systems 175 Online Menu browse SciStore.com 226 CambridgeSoft homepage 227 ChemOffice SDK 227 CS technical support 224 lookup suppliers on SciStore.com 225 register online 223 Online menu ACX numbers 226 ACX structures 225 OOP see Out of Plane Bending Open shell 175 Optimal field 29, 107 Optimal measurements 107 Optimizing to a transition state 134, 182 Order of attachment, specifying 78 Origin atoms, Z-matrix 101 Out of plane bending, equations 141 Out-of-plane bending 287 Output panel 23 Ovality, ChemProp Std 206 Overlays 43 Overlays, hiding fragments 45 P Packbits, compression 120 Page size 117 Pan see Translate Parameter table fields 272 Parameter tables, overview 271 Parameters bond angle 29 bond length 29 creating 273 estimating 273 guessing 153, 161 MM2 161, 289 xiv• CambridgeSoft
MOPAC 294 setting 216 Partial charge atom size control 57 definition 52 pop-up information 105, 106 Partition coefficient 207 Paste command 127 Paste special 15 Performing a molecular dynamics computation 158 Perspective rendering 60 Pi atoms table 280 Pi bonds and atoms with pi bonds 141 Pi bonds table 271, 281 PI keyword 172 Pi orbital SCF computation 291 Pi system SCF equations 141 PIATOMS.TBL see Pi atoms table PIBONDS.TBL see Pi bonds table Planarity 107 PM3 150, 169, 200 PNG file format 121 Polarizability 188 Pop-up information 105 Positioning by bond angles 103 Positioning by dihedral angle 104 Positioning example 103 PostScript files, background color 60 Potential energy function, choosing 148, 167 Potential energy surfaces (PES) 130, 133 Potential functions parameters 293 PRECISE keyword 171, 172, 183 Pre-defined substructures 38 Previous Users, help for 11 Principal Moments of Inertia, ChemProp Std 206 Print command 118 Printing 118 background color 60 Properties selecting 215 sorting 215 tab, GAMESS 212 tab, Gaussian 202 tab, MM2 161 Properties tab 201 Property calculation definition 130 Property filters 215 Pro-R 102 Pro-S 102 Protein Data Bank File FORTRAN format 260 Protein Data Bank file 259 Protein Data Bank file format 126 Protein Data Bank Files 259 Proteins, highlighting binding sites 94 Publishing formats 119 Q Quality field 273 Quantum mechanical methods applications summary 131 Quantum mechanics, theory in Brief 143 Quartic stretching term 291 Queuing minimizations 153 QuickTime file format 121 R R* field 284 RECALC keyword 171, 183 Record order 278, 280, 281, 287, 288 Recording minimization 153 molecular dynamics 160 Rectification 27 Chem3D Chem3D 9.0.1 • xv
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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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Administrator Connection tables by
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Administrator FORTRAN Formats The F
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5 6 1.11606 3 109.41 5 109.41 -1 21
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Administrator 41 4 1 0 0 0 0 0 0 0
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Administrator 32 3 12 1 0 0 0 33 3
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Administrator 13 * 3D displacement
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Administrator The field value for C
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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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