
! build segment for AMBER force field
! has to be used with pdb2xplor.py to fill in place holders

segment
   name="%(segment_id)4s"                   ! segment_id
   chain
        link ppgp head - GLY tail + PRO end
        link ppgg head - GLY tail + GLY end
        link pepp head - * tail + PRO end
        link ppg2 head - GLY tail + * end
        link ppg1 head - * tail + GLY end
        link pept head - * tail + * end

        coordinates @%(segment_pdb)s        ! take sequence from PDB
    end
end

%(amber_patch)s

vector do (name="CD1") (name "CD"  and resname "ILE")  ! rename ILE CD to CD1

coordinates @%(segment_pdb)s                ! read coordinates

