From g_hbond -h
"OH and NH groups are regarded as donors, O is an acceptor always, N
is an acceptor by default, but this can be switched using -nitacc.
Dummy hydrogen atoms are assumed to be connected to the first
preceding non-hydrogen atom."
The two groups are to find hbonds between group A and group B. If you
want to find hbonds within group A, then you specify an index group
that contains group A two times.
I think that you want:
[ group ]
100 101 200
Then give group 2x as the identical index group.
PS, there were problems with g_hbond a few months ago reported on
list, I suggest that you check to ensure that these problems were fixed.
Chris.
-- original message --
Hi,
To help clarify my previous g_hbond question, I have these two groups
in my index file
[ a_100_a_101] # 100 is N, #101 is H
100 101
[ a_200 ] # 200 is O
200
when I ran g_hbond, I got "Found 1 donors and 2 acceptors". The part
that I don't quite understand is why it says 2 acceptors. Did I set up
the groups correctly?
Again, hope this clarifies my question.
Thanks for your insight.
Simon
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