Research: AMOEBA Reference Frame

1 After we got the moleculeMP2.log file, copy/pasting the new Cartesian coordinates out of the end of moleculeMP2.log into the new .xyz file named moleculeMP2sp.xyz.

2 Then we use one of TINKER's facilities XYZEDIT. It have many interactively selectable options, choose (13) Translate and Rotate to Inertial Frame. At the end of the editing process, a new version of the orginal .xyz file is written as output. In our case, we should have a file named moleculeMP2sp.xyz_2.

3 Copy the coordinates from the moleculeMP2sp.xyz_2 file to your moleculeMP2sp.com file as your input coordinates. And add the command "Nosymm" .In this way, we can make the frame consistent with TINKER's inertial frame.

See the molecule flips in following picture.