# system: 7mer peptide in a box of
# periodic water (1577 Waters)

# Read in the trajectory file 
# starting at 1
# 100 total snapshots
# consider each one 
#

trajin trj.5 1 100 10

# now do some H-Bond analysis

# specify the electron pair DONOR
#
donor mask :1-7@O
donor print
# specify the ACCEPTOR(s)
acceptor WAT O H1 
acceptor print
#acceptor WAT O H2 

# do the Hbond search/output

#hbond solventacceptor O H1 solventacceptor O H2 solventneighbor 2 series hbond
hbond