Hello, all,
I use the Ptraj to do the Hbond analysis, when I run it, it says:
HBOND output to file output_hbond1.dat,
data will be sorted, intra-residue interactions will NOT be included,
...........
I only calculate in the same residue (MIC), I don't know why it doesn't calcuate the Intra-residue interactions.
Below is my input file. Do you think there is something wrong there? One more questions: what's the meaning of "series" in the H-bond analysis command? Thanks a lot for your help!
# calculate the H-Bond
trajin md.mdcrd
# specify the electron pair DONOR
donor MIC O15
# specify the ACCEPTOR(s)
acceptor MIC N6 H118
acceptor MIC N7 H129
acceptor MIC N4 H79
acceptor MIC N5 H90
acceptor MIC N2 H40
acceptor MIC N3 H51
acceptor MIC N H
acceptor MIC N1 H11
donor print
acceptor print
hbond out output_hbond1.dat
go
Esther B.
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Received on Sun Dec 03 2006 - 06:07:40 PST
