Because BOSS is written in Fortran, the position of fields in the parameter file should be kept as is. The optional last column is for comments. The first column defines the bonds and angles by atom classes, the second column gives the harmonic force constant and the third column gives the reference bond length or angle values. You can inspect this file by typing more etoh_oplsaa.sb into the UNIX shell. For the purpose of the tutorial, a simplified copy of the parameter file is provided by retaining only the parameters needed to describe ethanol. Inspect the bond stretching and angle bending parameter file. BOSS z-matrices can be generated from other coordinate files using the program autozmat. MOLDEN provides a graphical interface that facilitates construction of z-matrices. The z-matrix is a very important concept in computational chemistry and you need to understand how to construct z-matrices. For example, the sixth atom (C of CH3, atom type 135) is connected to the fifth atom (C of CH2, atom type 157) by a bond that is 1.53 Ang long, forms an angle of 108.9° with the first atom (O, atom type 154) and forms a torsional angle of 180° with the fourth atom (H, atom type 155). The Z-matrix format defines the structure via connectivity of atoms using the distance, angle, and torsion. The molecular structure is described in the Z-matrix format. Inspect the structure file, named here etoh.z. Change into this subdirectory and verify that you have eight files. etoh should create subdirectory etoh and copy the needed files.
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