containing RMSF of atomic fluctuations. Finally, there remains the
question of intermolecular contacts. These can be obtained from
the following script:trajin complex5.mdcrd 3001 10000 10
#-- 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@HD1acceptor 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
# in this example res181 is supposed to be PRO and excluded
donor mask @O
acceptor mask :2-180,182-290@N :2-290@H168 Gre ́gory Menchon et al.