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- ptr.tpl file is created for PTR, PHOSPHOTYROSINE - Rodney 02/28/2007
- Tyrosine can become phosphorylated through the action of a tyrosine kinase. In its phosphorylated form, it can be referred to as phosphotyrosine.
- PTRBK: neutral backbone.
- PTR01: neutral sidechain.
- PTR-1: neutral sidechain with anionic state: -1 charge on phosphoryl group.
- PTR-2: neutral sidechain with anionic state: -2 charge on phosphoryl group.
- Charge on the phosphate group is taken from GROMACS (GROMOS87):<http://www.gromacs.org/contributed_by_users/task,cat_view/gid,37/limit,5/limitstart,0/order,name/dir,ASC/) Energetics of Nucleophile Activation in a Protein Tyrosine Phosphatase; Hansson, Nordlund, and Åqvist; Journal of Molecular Biology, 265, 118-27, 1997.