Align two molecules

Table of Content

• Align two molecules
  • Table of Content
  • Aim and References
  • Usage
  • Examples with Screenshots

Aim and References

• Overlap two rigid bodies by translation followed by rotation (Kabsch algorithm).
• Supporting information of Construction of Two-Dimensional Potential Energy Surfaces of Reactions with Post-Transition-State Bifurcations.
• Appendix A of author's dissertation.
• Author : Hsiao-Han (Grace) Chuang

Usage

• In /src, both overlap.f90 and overlap.py do the same things; overlap two ridge bodies.

• Use makefile to compile Fortran code.

• Input:

  1. Structure to be varied: $1, extension: .xyz
  2. Reference structure; $2, extension: .xyz

Examples with Screenshots

Prepare two input files for program overlap.py or overlap.f90, and above input files follow the standard file format which can also be executed by general visualizer, like jmol.

The first input file is coord_from_output_S0.xyz in folder ./run, which has C-O bond length as 0.121 nm. This is the structure to be varied.

The second input file is coord_from_input_S0.xyz in the same folder as above file, which has C-O bond length as 0.123 nm. This is the reference structure.

Execute the program and change the coordinate of coords_from_output_S0.xyz into shifted.coords_from_output_S0.xyz. The screenshots of python and Fortran are shown as followed.

Execute the python code overlap.py, and it prints out the initial/final RMSD and also produces shifted structure as followed.

And then, Fortran code is executed to compare with python result, which is the same for both initial/final RMSD and shifted structure.

After translation and rotation, RMSD changes from 1.1677 to 0.0482, and the characteristic bond length of C-O is still reserved.