AIM: A Mapping Program for Infrared Spectroscopy of Proteins

Here, we present a new analysis program, AIM, that allows extracting thevibrational amide-I Hamiltonian using molecular dynamics trajectories for protein infraredspectroscopy modeling. The constructed Hamiltonians can be used as input for spectralcalculations allowing the calculation of infrared absorption spectra, vibrational circulardichroism, and two-dimensional infrared spectra. These spectroscopies allow the study of thestructure and dynamics of proteins. We will explain the essence of how AIM works and give examples of the information and spectra that can be obtained with the program using theTrypsin Inhibitor as an example. AIM is freely available from GitHub, and the packagecontains a demonstration allowing easy introduction to the use of the program.

Automated summary

This paper presents a new analysis program called AIM, which allows extracting the vibrational amide-I Hamiltonian for protein infrared spectroscopy modeling using molecular dynamics trajectories. The program enables the calculation of infrared absorption spectra, vibrational circular dichroism, and two-dimensional infrared spectra, facilitating the study of protein structure and dynamics. AIM is freely available on GitHub and includes a user-friendly demonstration.