remarks file toppar/protein.link
remarks 
remarks this is a macro to define standard protein peptide bonds
remarks and termini to generate a protein sequence.
 
set echo=false end

checkversion 0.9

link ACEP    head - ACE   tail + PRO     end
link ACEP    head - ACE   tail + CPR     end
link ACEL    head - ACE   tail + *       end

link NHHP    head - PRO   tail + NHH     end
link NHHP    head - CPR   tail + NHH     end
link NHHL    head - *     tail + NHH     end

link pepp    head - *     tail + pro     end  { link to pro }
link pepp    head - *     tail + cpr     end  { link to cpr }

link pept    head - ala   tail + *     end
link pept    head - arg   tail + *     end
link pept    head - asn   tail + *     end
link pept    head - asp   tail + *     end
link pept    head - cys   tail + *     end
link pept    head - gln   tail + *     end
link pept    head - glu   tail + *     end
link pept    head - gly   tail + *     end
link pept    head - hish  tail + *     end
link pept    head - his   tail + *     end
link pept    head - ile   tail + *     end
link pept    head - leu   tail + *     end
link pept    head - lys   tail + *     end
link pept    head - met   tail + *     end
link pept    head - mse   tail + *     end
link pept    head - m3l   tail + *     end
link pept    head - phe   tail + *     end
link pept    head - pro   tail + *     end
link pept    head - cpr   tail + *     end
link pept    head - ser   tail + *     end
link pept    head - thr   tail + *     end
link pept    head - trp   tail + *     end
link pept    head - tyr   tail + *     end
link pept    head - val   tail + *     end

first prop    tail + pro       end  { nter for pro }
first prop    tail + cpr       end  { nter for cpr }

first nter    tail + ala       end
first nter    tail + arg       end
first nter    tail + asn       end
first nter    tail + asp       end
first nter    tail + cys       end
first nter    tail + gln       end
first nter    tail + glu       end
first nter    tail + gly       end
first nter    tail + hish      end
first nter    tail + his       end
first nter    tail + ile       end
first nter    tail + leu       end
first nter    tail + lys       end
first nter    tail + met       end
first nter    tail + mse       end
first nter    tail + m3l       end
first nter    tail + phe       end
first nter    tail + ser       end
first nter    tail + thr       end
first nter    tail + trp       end
first nter    tail + tyr       end
first nter    tail + val       end

last cter    head - ala       end
last cter    head - arg       end
last cter    head - asn       end
last cter    head - asp       end
last cter    head - cys       end
last cter    head - gln       end
last cter    head - glu       end
last cter    head - gly       end
last cter    head - hish      end
last cter    head - his       end
last cter    head - ile       end
last cter    head - leu       end
last cter    head - lys       end
last cter    head - met       end
last cter    head - mse       end
last cter    head - m3l       end
last cter    head - phe       end
last cter    head - pro       end
last cter    head - cpr       end
last cter    head - ser       end
last cter    head - thr       end
last cter    head - trp       end
last cter    head - tyr       end
last cter    head - val       end

set echo=true end