Chem3D 8.0 Manual - CambridgeSoft

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Administrator18. Line 49 contains a listing of all the possiblefields for the bond list section. When the file iscreated by Chem3D Pro the following fields areused: Bond#, Bond_type, atom 1, atom 2 andcis/trans and Qorder.19. Lines 50–68 each contain 4 fields describinginformation about each of the bonds in thestructure: the first field is the internal bondnumber (6), the second field is the bond type(1), the third and fourth fields are the atomserial numbers for the atoms involved in thebond [atom 1 (2), atom 2 (16)], the fifth field isthe cis/trans designator (this is 0 if it does notapply), the sixth through tenth fields areignored, and contain zeros if the file is createdusing Chem3D Pro, the eleventh field containsthe bond order ([S] meaning single), the twelfthand thirteenth fields are ignored and containzeros if the file is created using Chem3D Pro.20. Lines 69–73 are each a section header for 3Dconversion use. This section only contains theheader name only (as shown) when the file iscreated using Chem3D Pro.21. Line 74 is a header for the section User dataarea. This section contains the header nameonly (as shown) when the file is created usingChem3D Pro.22. Line 75 is a header that indicates the End ofFile.FORTRAN FormatsThe FORTRAN format for each record of theMolecular Simulations MolFile format is as follows:LineNumberMOPACDescription29-47 atom list, fieldvalue50-68 bond list, fieldvaluesFORTRANFormatI,1X,A,3(1X,I),3F9.3,1X,I,F4.1,7(1X,I),1X,A,I,8(1X,I),“[“,A, “] “I,4(1X,I),F9.3,4(2X,I),1X, “[“,A1, “]“,2(1X,I)The specific format of the MOPAC files used byChem3D is the MOPAC Data-File format. Thisformat is described on pages 1-5 through 1-7 of the“Description of MOPAC” section and page 3-5 ofthe “Geometry Specification” section in theMOPAC Manual (fifth edition). For further detailsabout the MOPAC Data-File format, please refer tothe above publication.The following is a sample MOPAC output file fromChem3D for cyclohexanol:Line 1:Line 2: CyclohexanolLine 3:Line 4a: C 0 0 0 0 0 0 0 0 0Line 4b: C 1.54152 1 0 0 0 0 1 0 0Line 4c: C 1.53523 1 111.7747 1 0 0 2 1 0Line 4d: C 1.53973 1 109.7114 1 -55.6959 1 1 2 3A50 • CambridgeSoftMSI MolFile
Line 4e: C 1.53597 1 111.7012 1 55.3112 1 4 1 2Line 4f: C 1.53424 1 110.7535 1 57.03175 1 3 2 1Line 4g: O 1.40196 1 107.6989 1 -172.662 1 1 2 3Line 4h: H 1.11739 1 107.8685 1 62.06751 1 1 2 3Line 4I: H 1.11633 1 110.0751 1 -177.17 1 2 1 4Line 4j: H 1.11566 1 109.4526 1 65.43868 1 2 1 4Line 4k: H 1.11665 1 109.9597 1 178.6209 1 3 2 1Line 4l: H 1.1161 1 109.5453 1 -63.9507 1 3 2 1Line 4m: H 1.11542 1 109.4316 1 -66.0209 1 4 1 2Line 4n: H 1.11499 1 110.549 1 176.0838 1 4 1 2Line 4o: H 1.11671 1 109.93 1 -178.296 1 5 4 1Line 4p: H 1.11615 1 109.4596 1 64.43501 1 5 4 1Line 4q: H 1.11664 1 110.0104 1 -178.325 1 6 3 2Line 4r: H 1.11604 1 109.6082 1 64.09581 1 6 3 2Line 4s: H 0.94199 1 106.898 1 -173.033 1 7 1 2The following illustrates the components of theMOPAC Output File from Chem3D for C(1)Through C(4) of Cyclohexanol1st Atom2nd Atom3rd Atom4th AtomElementSymbolCCCCBondLengths0.0000001.5415191.5352331.539734ActionIntegers0111BondAngles0.0000000.000000111.774673109.711411ActionIntegersDihedralAnglesActionIntegersThe internal coordinates section of the MOPACData-File format contains one line of text for eachatom in the model. Each line contains bond lengths,bond angles, dihedral angles, action integers, andconnectivity atoms.0010.0000000.0000000.0000001 -55.695877 1000ConnectivityAtoms0 0 01 0 02 1 01 2 3As shown in the illustration above, C(1) is the originatom. C(2) is connected to C(1) with a bond oflength 1.541519 Å. C(3) is connected to C(2) with abond of length 1.535233 Å, and is at a bond angle of111.774673 degrees from C(1). C(4) is connected toC(1) with a bond of length 1.539734 Å, and is at abond angle of 109.711411 degrees from C(2). C(4)also forms a dihedral angle of-55.695877 degrees with C(3).The action integers listed next to each measurementare instructions to MOPAC which are as follows:1Optimize this internal coordinate0Do not optimize this internal coordinate-1Reaction coordinate or grid indexWhen you create a MOPAC file from withinChem3D, an action integer of 1 is automaticallyassigned to each non-zero bond length, bond angle,and dihedral angle for each atom record in the file.AppendixChem3D 8MSI MolFile• A51
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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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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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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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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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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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To remove all frames after the fram
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Administrator106 • Chapter 7: Ins
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If you want to …Then select …Fi
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AdministratorBMPThe Bitmap file for
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When you save a file as a Connectio
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AdministratorIf you want to …buil
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Administratorexports .PDB. The .PDB
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Administrator116 • Chapter 8: Pri
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AdministratorComputational Chemistr
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AdministratorThe following table su
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Administrator• A single point cal
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Administrator• Potential energy f
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AdministratorE Stretch= 71.94 ∑ K
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Administratorwhich are used to scal
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AdministratorQuantum mechanical met
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AdministratorUHFThe UHF method trea
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Administrator• Hypervalent compou
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Administrator138 • Chapter 9: Com
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AdministratorIf you want to …spec
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AdministratorThe Total Steric Energ
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AdministratorThe conformation you c
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.AdministratorSticks < Ball and Sti
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AdministratorThe simulation ends wh
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AdministratorThe units are kcal/mol
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AdministratorRepeating an MM2Comput
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AdministratorTo determine the appro
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AdministratorFirst excited quintet:
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AdministratorMOPAC uses its default
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The heat of formation is composed o
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AdministratorComparing Cation Stabi
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Administratormeta>para>ortho, where
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Administrator3. Click in the model
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Form ofglycine∆H(kcal/mole)Solven
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AdministratorThe following table co
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AdministratorThe Message window dis
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AdministratorDescriptionVibrational
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You can create a structure from the
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AdministratorIf you want to …reco
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AdministratorSave a customized job
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Administrator2. Type the full path
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Administrator3. From the Basis Set
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AdministratorA new model window is
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PropertyDescriptionPropertyDescript
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PropertyDescriptionError MessageCau
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PropertyDescriptionThe GAMESS serve
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The property filters are:Administra
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AdministratorTo perform property ca
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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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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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