Dear amber users
If I want to use ptraj for water-mediated hydrogen bond analysis, in input
file after donor and acceptor mask which of what being below is true?
1-
hbond print 0.05 series hb.out
2-
hbond solventdonor WAT O solventacceptor WAT O H1 solventacceptor WAT O H2
hbond print 0.05 series hb.out
3-
hbond solventneighbor 6 solventdonor WAT O solventacceptor WAT O H1
solventacceptor WAT O H2
hbond print 0.05 series hb.out
what means of solventneighbor 6? what number is true?
if all of above is unsuitable, please guide me.
best regards
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
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Received on Thu Mar 03 2011 - 05:30:02 PST
