Download and Copy ProteinFishing.pdb and ProteinFishing.cfg into your working directory and type:

./modelX -f ProteinFishing.cfg

Or check the command line tab
Name Parameter Description Parameter Type Parameter Default Parameter Range
atom-type Atom type to be consider in the evaluation: BB,SC,ALL string BB 0-2
biassed Use biassed or non biassed forcefield bool false
command string
config Set a configuration file path
database-name Set the mySQL database name string PepXDB
database-pass Set the mySQL password string modelx
database-port Set the mySQL database port int 3306
database-server Set the mySQL server string localhost
database-user Set the mySQL username string modelx
excluded File with excluded pdb from queries path
help Show help screen
max-threads Set the maximum number of threads int 1
output-dir Set output directory path
output-file Get Pdb file without dna path noDna.pdb
pdb Set a PDB file path
pdb-dir Set PDB directory path
renumber Renumber the pdb bool false
>modelx --command=ProteinFishing --pdb=ProteinFishing.pdb --residue-begin=89 --residue-end=94 --hook-mol=C --fisher-mol=A --dubiety=0.4 --pep-mismatches=6 --contact-th=10 --cbeta-angles=10 --sections=37 --fit-threshold=1 --fit-level=1 --biassed=false --database-name=FishXDB --database-server=localhost --database-user=modelx --database-pass=modelx