Running DockSorter with the predictions provided by EpiPred

java -jar DockSorterConstr.jar -abf AB_sol.pdb -agf AG_sol.pdb -abc A -agc B -constab paratope_const.txt -constag epitope_const.txt -quiet

Options and their associated arguments:

abf: antibody file
agf: antigen file
abc: antibody chains (e.g. 'HL' or 'A' as above) 
agc: antigen chains (e.g. 'CD' or 'B' as above)
constab: antibody constraint (see below)
constag: antigen constraint (see below)
quiet: non-verbose mode

Paratope file:

Examine the paratope_const.txt supplied with the program to get an idea of what goes into it. In the example, we are using antibody with chain A. Thus, we specify residues on chain A that are considered contacting residues and we specify them by giving the chain id and the residue id as in:

55[whitespace]A - means residue 55 on chain A in the supplied antibody file is considered to be a contact residue.

Epitope file:

Format is identical as for paratope. See file epitope_const.txt supplied with the program to see an example.
