11/28/2023 0 Comments Zmatrix water![]() This will likely fail on your input with an error: Therefore you also need to tell Gaussian to rebuild it ( -rebuildzmat). In Gaussian terms, a block of cartesian coordinates is also a z-matrix. This means the first line denotes the number of atoms, the second line denotes a comment, and both need to be skipped. The format you have posted is actually (simple) xmol. Kalju Kahn, Department of Chemistry and Biochemistry, UC Santa Barbara.According to the manual of the newzmat utility of Gaussian 16, it accepts unadorned Cartesian coordinates ( G16 online manual). If you have installed a molecular mechanics program such as TINKER, you may be able to perform a molecular mechanics minimization from within MOLDEN. You can close the Z-matrix editor and write the structure out in a common file format such as PDB, MOL2, or MOL. For example, you save the coordinates as Z-matrix input file for quantum chemistry programs such as Gaussian or GAMESS. You can do several things with the structure you have created. 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 in ethanol with the methyl group.
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