abinitio

Usage: modelmaker abinitio -model <full length template pdb> -fragfiles <list of fragment files>
-sel <list of atomselection texts with selections to fold> -anchor <atomselection text for anchor residue for coordinate restraints>
?options?
Options: -jobname <name prefix for job> (default: taken from -model)
-workdir <working/project directory for job> (default: $DefaultWorkDir)
-nstruct <number of structures to predict> (default: $DefaultNStruct)
-testrun <test run flag (0 or 1)> (default: $DefaultTestRun)
-np <Number of processors to use. MPI version only>

An example of how to use ModelMaker to fold protein termini from the tutorial is below:

modelmaker abinitio -np 4 -model rpn11_18-306_full_length.pdb -jobname rpn11_18-306 -anchor "resid 200" 
-fragfiles {{rpn11_280-306.frag9 rpn11_280-306.frag3}} -sel "resid 288 to 306" -nstruct 4