But the output file doesn't contain the fragment that should say that all 4 convergence criteria are satisfied and that a stationary point is located. What's even weirder is that it seems to happen right after everything is already calculated (all the energies and corrections). This error occurs in the frequency calculation. Kalju Kahn, Department of Chemistry and Biochemistry, UC Santa Barbara.I'm doing my calculations using G09W. 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.
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