trajin 2a6_md2_nowat.mdcrd #-- Donors from standard amino acids donor mask :GLN@OE1 donor mask :GLN@NE2 donor mask :ASN@OD1 donor mask :ASN@ND2 donor mask :TYR@OH donor mask :ASP@OD1 donor mask :ASP@OD2 donor mask :GLU@OE1 donor mask :GLU@OE2 donor mask :SER@OG donor mask :THR@OG1 donor mask :HIS@ND1 donor mask :HIE@ND1 donor mask :HID@NE2 #-- Acceptors from standard amino acids acceptor mask :ASN@ND2 :ASN@HD21 acceptor mask :ASN@ND2 :ASN@HD22 acceptor mask :TYR@OH :TYR@HH acceptor mask :GLN@NE2 :GLN@HE21 acceptor mask :GLN@NE2 :GLN@HE22 acceptor mask :TRP@NE1 :TRP@HE1 acceptor mask :LYS@NZ :LYS@HZ1 acceptor mask :LYS@NZ :LYS@HZ2 acceptor mask :LYS@NZ :LYS@HZ3 acceptor mask :SER@OG :SER@HG acceptor mask :THR@OG1 :THR@HG1 acceptor mask :ARG@NH2 :ARG@HH21 acceptor mask :ARG@NH2 :ARG@HH22 acceptor mask :ARG@NH1 :ARG@HH11 acceptor mask :ARG@NH1 :ARG@HH12 acceptor mask :ARG@NE :ARG@HE acceptor mask :HIS@NE2 :HIS@HE2 acceptor mask :HIE@NE2 :HIE@HE2 acceptor mask :HID@ND1 :HID@HD1 acceptor mask :HIP@ND1,NE2 :HIP@HE2,HD1 #-- Backbone donors and acceptors for this particular molecule # N-H for prolines do not exist so are not in the mask # donor mask @O acceptor mask :2-4,7,9,11,13-37,39-45,47-140,142-201,203,205-231,233-234,236-252,254-291,293-311,313-320,322-337,339-356,358-363,365-372,374-378,380-383,385-401,403-438,440-445,447-454,456-463,465@N :2-465@H #Terminal residues have different atom names donor mask @OXT acceptor mask :1@N :1@H1 acceptor mask :1@N :1@H2 acceptor mask :1@N :1@H3 #-- series hbt is just a placeholder to ensure we get the full analysis. If you don't #have the word series you don't get a full analysis. hbond print .25 series hbt