> Hi I am trying to do a hydrogen bond analysis using ptraj. I want to track
> if specific atoms are making hydrogen bond contacts during the trajectories.
> However I notice that the ptraj script I am using reads in the donors and
> the acceptors and then returns any hydrogen bonds that they make. I want the
> first donor and first acceptor listed to specify a hydrogen bond, second
> donor and second acceptor to track another hbond, etc. Is there any way to
> do this?
No, not directly; the intent of the h-bond functionality is to be
able to see all (relevant) h-bonds to groups of interest, not just
the 1-1 mapping.
To get the information you want, either:
(1) you will have to create a separate script for each h-bond of interest
(which is tedious)
or
(2) simply track distances (and possibly angles) for the h-bond of
interest
trajin traj
distance hb1 :1.O :100.N out d1.dat
distance hb2 :2.O :101.N out d2.dat
analyze statistics all
--tec3
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Received on Fri Feb 20 2009 - 01:11:17 PST
