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

Download:

Atom definitions for MLY, M2L, M3L, ACK, ARM, SRM, DRM.
Amber library files for MLY, M2L, M3L, ACK, ARM, SRM, DRM.
Additional frcmod file for DRM.
Sample tleap input file.
Tinker parameter file for all seven modified amino acids.

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Last update: Mar 27, 2013 13:46:22