Dimitris Papageorgiou Dept. of Materials Science and Engineering
University of Ioannina, Greece

AMBER parameters for modified amino acids

The following is a collection of library files for the AMBER (parm99) force field. Seven modified amino acids are considered:
  • Mono-methylated lysine (MLY)
  • Di-methylated lysine (M2L)
  • Tri-methylated lysine (M3L)
  • Acetylated lysine (ACK)
  • Mono-methylated arginine (ARM)
  • Symmetrically di-methylated arginine (SRM)
  • Asymmetrically di-methylated arginine (DRM)
The library files are provided in a format suitable for the Amber (tleap) and Tinker software packages. Derivation of the partial charges is described in the following article:

Structural role of RKS motifs in chromatin interactions: A molecular dynamics study of HP1 bound to a variably modified histone tail
G.V. Papamokos,G. Tziatzos, D.G. Papageorgiou, S.D. Georgatos, A.S. Politou, E. Kaxiras
Biophysical Journal 102 (2012) 1926-1933.
DOI: 10.1016/j.bpj.2012.03.030

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