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Administrator 12. Line 30, “@BOND”, is a Record Type Indicator (RTI) which begins a section containing information about the bonds associated with the molecule. 13. .Lines 31–49 each contain 4 fields describing information about a bond: the first field is the bond id, the second field is the from-atom id, the third field is the to-atom id, and the fourth field is the bond type. 1 Molecule name (file name) 5 Number of atoms/number of bonds 11–29 Atom type, name, coordinates and id “# “,5X, “Name: “,1X,A 4(1X,I2) I4,6X,A2,3X,3 F9.3,2X,A5 FORTRAN Formats The FORTRAN format for each record of the SYBYL MOL2 File format is as follows: 31–49 Bond id, from-atom, to-atom, bond type 3I4,3X,A2 Line Number Description FORTRAN Format 648• File Formats CambridgeSoft Protein Data Bank Files
Appendix G: Parameter Tables Parameter Table Overview Chem3D uses the parameter tables, containing information about elements, bond types, atom types, and other parameters, for building and for analyzing your model. The parameter tables must be located in the C3D Items directory in the same directory as the Chem3D application. Parameter Table Use Chem3D uses several parameter tables to calculate bond lengths and bond angles in your model. To apply this information, select Apply Standard measurements in the Building Control panel. Calculating the MM2 force field of a model requires special parameters for the atoms and bonds in your model. The MM2 force field is calculated during Energy Minimization, Molecular Dynamics, and Steric Energy computations. The use of the parameter tables are described in the following table: Parameter Table Use Parameter Table 4-Membered Ring Angles.xml 4-Membered Ring Torsionals.xml Angle Bending Parameters.xml Atom Types.xml Bond Stretching Parameters.xml Use Bond angles for bonds in 4-membered rings. In force field analysis, angle bending portion of the force field for bonds in 4-membered rings. Computes the portion of the force field for the torsional angles in your model for atoms in 4-membered rings. Standard bond angles. In force field analysis, angle bending portion of the force field for bonds. Contains atom types available for building models. Standard bond lengths. In force field analysis, bond stretching and electrostatic portions of force field for bonds. 3-Membered Ring Angles.xml Bond angles for bonds in 3-membered rings. In force field analysis, angle bending portion of the force field for bonds in 3-membered rings. Conjugated Pisystem Atoms.xml Bond lengths for bonds involved in Pi systems. Pi system portion of the force field for pi atoms. Appendices ChemOffice 2005/Appendix Parameter Tables • 649 Parameter Table Use
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