Kalju Kahn, Department of Chemistry and Biochemistry, UC Santa Barbara. Close MOLDEN the optimized structure was saved on your directory in the file isopropanol.xyz. Keep other settings at default values and press GO to optimize the structure. Another useful force field is the Tripos/Sybyl force field that should be selected for molecules that you are not planning to minimize with TINKER. The MM3 is one of many molecular mechanics force fields and is suitable for modeling simple organic compounds. Select Tinker MM3 force field for optimization.This feature works nicely with simple molecules but most likely you are not able to use MOLDEN/TINKER for automatic optimization of more complex organic molecules because of the lack of force field parameters. This brings up Molecular Mechanics Force Field tools that allow assignment of the force field atom types and optimization of molecular geometry. Click on the FF icon in the MOLDEN Control window.Close the Z-matrix editor but do not exit MOLDEN.Notice how the new atoms appear in the Z-matrix editor and in the MOLDEN graphical window. Use Substitute Atom by Fragment function to replace one of the CH 2 hydrogens with the methyl group.Follow the instructions below to create isopropanol (2-propanol) by modifying the structure of ethanol. Please note that it is recommended to assign a SYBYL force field to the modified molecule every time before writing out a new structure as MOL2 file even if you are not planning to optimize the molecule. For example, you may notice that more hydrophobic analogs of a drug are more potent and wish to create a higher homolog of your lead compound by extending or branching the alkyl chain. Oftentimes you have a structure that you want to modify slightly. For highly symmetric molecules, or with molecules with linear groups (such as acetonitrile) use of dummy atoms to define the position of first few real atoms.However, dihedral angles can have any value between -360 and +360. All bond angles should be less than 180 degrees.For example, to draw the gauche form of ethanol, you may change the dihedral angle for the OH hydrogen (the HO-CC torsion) to 60 degrees. Usually, dummy atoms are placed at 90 degrees to a pair of atoms and the third collinear atom is then defined with a bond angle of 90 degrees and a dihedral of 0 or 180 degrees with respect to the previous 3 atoms. You may adjust bond lengths and bond angles to reflect the local geometry of the molecule.As mentioned in the comment by Fl.pf, the program molden has a very powerful ZMAT Editor: You can hand pick the atoms that define bond lengths, angles and dihedrals. Here you can format and select z-matrix for Gaussian input. When replacing an atom with fragment, click on the atom to be replaced, then select the fragment. Just draw the molecule, then navigate to menu Extensions Gaussian.When adding a new atom, click on the atom it is connected to, then on the atom it makes an angle with, then on the atom it forms dihedral angle with.You may occasionally need to use Reorder Z-matrix to achieve desired symmetry or when needing to delete atoms that are used to define position of other atoms. The Substitute Atom by Fragment allows replacement of atoms with common functional groups. The command Add Line adds a new atom in the molecule and creates a new line in the Z-matrix.The few rules that you should keep in mind when working with Z-matrixes are: The Zmatrix editor in Molden is pretty simple to learn. You can measure arbitrary distances easily using the Distance tool in the Molden Control panel. Now click on the bond distances fields in the Z-Matrix editor and notice how the two connected atoms are highlighted. It also works in reverse: clicking on an atom in the 3D structure will highlight this atom in the Z-matrix. Inspect the Z-Matrix by clicking on each atom and observe how the selected atom is highlighted in the graphical window. Answer Yes if prompted to create a new Z-matrix. Hit the ZMAT Editor button to open the Z-Matrix editor. Turn on StickColor and try if the molecule looks better with Shade on or off. Two windows, the graphical area and the Molden Control appear. Start MOLDEN by typing molden ethanol.pdb into Unix shell on the workstation. You should have a structure of ethanol saved in your folder as a PDB file. MOLDEN's Z-matrix editor is explained in more detail at. In the Z-matrix notation, the atoms in the molecule are defined by bond a length to one of the preceding atoms, by a bond angle made to two preceding atoms and by a dihedral angle made to three preceding atoms. MOLDEN allows building molecules using the connectivity description known as the Z-matrix. The last part of this tutorial illustrates how MOLDEN can be used to optimize molecular structures and prepare molecules for more advanced calculations. This tutorial illustrates how to edit and build molecular structures with MOLDEN. Building Molecules with MOLDEN Building Molecules with MOLDENĪbility to build molecular models with computers in an important skill for chemists who use computer-aided drug design.
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