GHlacour / AmideImaps

Utility program for GROMACS calculating the amide I Hamiltonian for peptides and proteins

AmideImaps

Utility program for GROMACS calculating the amide I Hamiltonian for peptides and proteins.

AIM

AmideImaps is only working for older versions of GROMACS. Checkout our new programme AIM, which can also use trajectories from newer versions and from other MD packages: https://github.com/Kimvana/AIM

Functionality of AmideImaps

The program utilize mappings for the amide I mode of proteins as described in the papers below:

1. T. L. C. Jansen and J. Knoester. A transferable electrostatic map for solvation effects on amide I vibrations and its application to linear and two-dimensional spectroscopy. J. Chem. Phys., 124:044502, 2006.
2. T. L. C. Jansen, A. G. Dijkstra, T. M. Watson, J. D. Hirst, and J. Knoester. Modeling the amide I bands of small peptides. J. Chem. Phys., 125:044312, 2006.
3. S. Roy, J Lessing, G Meisl, Z Ganim, A Tokmakoff, J Knoester, and T. l. C. Jansen. Solvent and Conformation Dependence of Amide I Vibrations in Peptides and Proteins with Proline. J. Chem. Phys., 135:234507, 2011.
4. L. Wang, C. T. Middleton, M. T. Zanni, and J. L. Skinner. Development and Validation of Transferable Amide I Vibrational Frequency Maps for Peptides. J. Phys. Chem. B, 115:3713, 2011.
5. H. Torii and M. Tasumi. Ab initio molecular orbital study of the amide I vibrational interactions between the peptide groups in di- and tripeptides and considerations on the conformation of the extended helix. J. Raman Spec., 29(1):81–86, 1998.
6. M. Reppert and A. Tokmakoff. Electrostatic frequency shifts in amide i vibrational spectra: Direct parametrization against experiments. J. Chem. Phys., 138:134116, 2013.