martinize2 
-f ../aa.pdb 
-ff martini3001 
-x cg.pdb 
-o topol.top 
-ignore HOH 
-ss CBCCHHHHHHHHHHTTCTTBTTBCHHHHHHHHHHHHTTBTTCEEECTTSCEEETTTTEETTTTCBCSCCTTCCCTTCSBGGGGGSSSCHHHHHHHHHHHHTSSGGGGSHHHHHHTTTSCGGGGGTTCCC 
-go ../map.map 
-noscfix
-cys none
-name molecule_0