Chem3D 8.0 Manual - CambridgeSoft

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AdministratorRepeating an MM2ComputationAfter you perform an MM2 computation, you canrepeat the job as follows:1. From the MM2 menu, choose Repeat MM2Job....The appropriate dialog box appears.2. Change parameters if desired and click Run.The computation proceeds.Using .jdf FilesYou can run MM2 computations on previouslycreated job description files (.jdf). The job type andsettings are saved in the .jdf file.To run an MM2 job:1. From the MM2 menu, choose Run MM2 Job.2. Choose the file and click Open.The dialog box for the appropriate computationappears.3. Change parameters if desired and click Run.152 • Chapter 10: MM2 Computations CambridgeSoftRepeating an MM2 Computation
Chapter 11: MOPAC ComputationsMOPAC OverviewMOPAC is a molecular computation applicationdeveloped by Dr. James Stewart and supported byFujitsu Corporation that features a number ofwidely-used, semi-empirical methods. It is availablein two versions, Standard and Professional.MOPAC Std. is available as an optional addin forChem3D Pro. MOPAC Pro is a standard feature ofChem3D Ultra. Sections labeled “Ultra” in thischapter refer to features found only in Chem3DUltra with MOPAC Pro. Sections without labelsrefer to the more limited features of MOPAC Std.Chem3D MOPAC provides a graphical userinterface (GUI) that allows you to perform MOPACcomputations directly on the model in the Chem3Dmodel window. As a computation progresses, themodel changes appearance to reflect the computedresult. Computations are limited in CS MOPAC to250 heavy atoms.The following procedure assume you have a basicunderstanding of the computational concepts andterminology of semi-empirical methods, and theconcepts involved in geometry optimization(minimization) and single-point computations. Formore information see “Chapter 9: ComputationConcepts.”The Chem3D CD-ROM contains the completeMOPAC manual in Adobe Acrobat PDF format. Themanual, along with the Adobe Acrobat Readerapplication, is in the folder named Documentation.Minimize EnergyMinimizing energy is generally the first molecularcomputation performed on a model.To minimize energy of a model:1. From the MOPAC menu, choose MinimizeEnergy.The Minimize Energy dialog box appears.The Job Type TabUse the Job Type tab to set options for display andrecording results of calculations, and to enter theMinimum RMS Gradient value.Chem3D 8 Chapter 11: MOPAC Computations • 151Minimize Energy
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ChemOffice.Com®ChemOffice®Chem3D,
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CS Product RegistrationRegistering
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User’s GuideCS Chem3D 8.0for Wind
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CambridgeSoft Software License1. Gr
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No Waiver. The failure of either pa
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The failure of either party to asse
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ContentsIntroduction . . . . . . .
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Rotating Fragments. . . . . . . . .
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Choosing a Hamiltonian . . . . . .
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Appendix D: MM2 . . . . . . . . . .
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Administrator• Faster graphics-3D
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AdministratorInstallation and Syste
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AdministratorModel WindowThe Model
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Table ElementDescriptionObjectDescr
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To specify the rendering type, atom
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AdministratorYou can also build mod
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AdministratorElementBound-to orderS
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Customizing the UserInterfaceAdmini
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AdministratoroptionUse BackBuffer f
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AdministratorExamine the atoms and
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Administrator2. Release the mouse b
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AdministratorReplacing AtomsTo chan
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Change the model display type:Build
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You will also save the frames you c
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Tutorial 4: SearchingFor Conformati
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Administrator3. Click in the model
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Administrator5. In the Theory tab,
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AdministratorFor phenol, the greate
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Creating a Model UsingTemplatesChem
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The Cartesian Coordinates Options d
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Saving a Model with a Different Nam
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Administrator44 • Chapter 3: Crea
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AdministratorThe following table de
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After you have the backbone, you ca
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AdministratorThe interpretation of
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AdministratorTo use a substructure
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AdministratorThe standard measureme
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AdministratorTo change the bond ord
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Administratorvalues are the standar
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AdministratorTo remove the formal c
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AdministratorRefining a ModelAfter
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AdministratorSelecting Atoms in a G
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AdministratorWhen you choose Show A
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AdministratorTo perform a rotation
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To move three atoms to a plane and
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Administratorit and other atoms. Al
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AdministratorIf an atom is position
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AdministratorModel TypesThe followi
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AdministratorColoring DisplaysYou c
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To change one of the colors in the
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AdministratorAll atoms currently in
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AdministratorDisplaying MolecularSu
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AdministratorMolecular Surface Colo
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AdministratorSolvent Accessible Sur
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AdministratorTo display a Connolly
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previously computed surface. If you
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If you want todisplay …Then Selec
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Administrator• From the Edit menu
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AdministratorShowing Dihedral Angle
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Administrator5. Select the C(2)-C(3
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AdministratorThe color of the atoms
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AdministratorTo begin the docking c
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AdministratorTo perform an overlay,
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To remove all frames after the fram
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The Select Descriptors dialog box a
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Administrator• Sum• Standard de
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To access Browse ChemStore.com:The
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AdministratorTo access the ChemOffi
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AdministratorDefining Substructures
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AdministratorA4 • CambridgeSoftDe
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AdministratorIf an atom can be assi
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AdministratorExample 3In Example 3,
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AdministratorEditing ParametersYou
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Administrator5. A matrix called the
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AdministratorAdding Parameters toMO
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AdministratorParameter Table UseEle
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AdministratorThe ElementsThe Elemen
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AdministratorTo view the menu of ge
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AdministratorFinally, the 1-19 bond
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AdministratorPi AtomsThe Pi Atoms t
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AdministratorCubic and Quartic Stre
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potential well increases, as does t
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AdministratorThe counterintuitive f
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Administratorcorrespondence between
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AdministratorAlchemy FileThe follow
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Administrator2. The first line of a
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H 102 2.127594 1.865631 1.48999 21
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Administrator6 1 1.40195 2 107.6989
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41 3 1 0 0 0 0 0 0 0 0 0 0 1.222366
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Administrator21 -1.2615 2.1277 0.01
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Administrator24-42 Bond id, fromato
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Administrator51 2 1 1 6 0 0.000 0 0
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Administrator18. Line 49 contains a
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AdministratorFORTRAN FormatsThe des
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22 Chain Identifier No12-16 Serial
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AdministratorLine 18 H 0 0 0Line 19
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Administratorof hydrogens attached
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AdministratorNumberof AtomsNumberof
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AdministratorLine 30 @BONDLine 31 1
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11-29 Atom type, name,coordinates a
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AdministratorA66 • CambridgeSoftW
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AdministratorTroubleshootingThis se
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4. If the problem still occurs, Fax
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AdministratorAtom typesassigning au
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Administratorchem3d.h 17chem3d.tlb
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AdministratorDisplay Stereo View 80
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AdministratorFont 16Font size 16For
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Administratorjdt file format 114, 1
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AdministratorMolecular Surfacescalc
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AdministratorParameters 12bond angl
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AdministratorSelect Fragment comman
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AdministratorTools palette 6, 44Too
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Administratorxx • IndexCambridgeS
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CAMBRIDGESOFTChemOffice Desktop toK
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CS ChemOfficeSoftware SuitesChemOff
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DESKTOPCS E-NotebookElectronic Jour
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DESKTOPCS ChemDrawChemical Structur
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DESKTOPCS Chem3DMolecular Modeling
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DESKTOPCS ChemFinderSearching and I
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DESKTOPCS ChemInfoReference and Che
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ENTERPRISEChemOffice WebServerEnter
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ENTERPRISEOracle CartridgeEnterpris
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KNOWLEDGEE-Notebook EnterpriseDeskt
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KNOWLEDGEDocument ManagerDesktop to
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KNOWLEDGE21CFR11 ComplianceElectron
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RESEARCH&Registration SystemChemica
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RESEARCH&Inventory ManagerChemical
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RESEARCH&CombiChem EnterpriseDeskto
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RESEARCH&BioAssay HTSBiological Ass
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RESEARCH&BioSAR BrowserBiological a
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CHEMICALChemACX DatabaseAvailable C
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CHEMICALThe Merck IndexChemistry’
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CHEMICALChemical DatabasesReference
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CONSULTING &Consulting & ServicesDe
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Administrator
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MENUSCreate a new model window.Open
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WORKING WITH SELECTIONSIf you want
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CS ChemOffice®Desktop to Enterpris
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