Keywords: AMBER, phosphorylation, phosphoserine, phosphothreonine, and phosphotyrosine
AMBER has many files that are required to be modified to implement the phoshorylated residues into a structure. First PDB files may need to be converted into AMBER nomenclature and hydrogen atoms added. This is done using the utility protonate which requires PROTON_INFO.
The construction of the prmtop file is done by the AMBER utility leap. We use a leaprc file the contains the directives for the leap program. The new library is appended to the internal datastructures of the program by the directive, loadOff amber_sep.lib.
Finally a MASTER.RST file is constructed from that concatenation of files generated by makeDIST_RST, makeANG_RST, and makeCHIR_RST. The program makeANG_RST uses the new.map and tors.lib databases.
A set of MATLAB scripts are also provided for others wanting to transform PDB files of other modified amino acids. Details are provided in the overview and README files.