Supplementary Information



All of the topology and parameter files below are to be used in conjunction with top_all27_prot_na.rtf and par_all27_na.prm.


Felix Autenrieth, Emad Tajkhorshid, Jerome Baudry, Zan Luthey-Schulten (last updated 2005)
Classical force field parameters for the heme prosthetic group of cytochrome c
Journal of Physical Chemistry B, 108, 20376-20387, 2004
Heme parameters
Heme topology


These parameters have been modified and extended to include Fe-S complexes (courtsey of Abhishek Singharoy)
Abhishek Singharoy, Angela M. Barragan, Sundaraphandian Thangapandian, Emad Tajkhorshid, Klaus Schulten
Binding Site Recognition and Docking Dynamics of a Single Electron Transport Protein: Cytochrome c2
J. Am. Chem. Soc., 2016, 138 (37), pp 120; DOI: 10.1021/jacs.6b0119377
Topology and parameters


Patrick Donoghue, Anurag Sethi, Carl R. Woese and Zaida Luthey-Schulten
The evolutionary history of Cys-tRNACys
Proc. Natl. Acad. Sci. U S A, 102(52):19003-19008, 2005
Aos/Spa parameters
Aos/Spa topology


J. Eargle, A. Black, A. Sethi, L. Trabuco, and Z. Luthey-Schulten
Dynamics of recognition between tRNA and Elongation Factor Tu
J. Mol. Biol., 377(5):1382-405, 2008
Paramter file for modified nucleosides
Topology file for modified nucleosides