AMBER Archive (2009)

Subject: Re: [AMBER] question about ptraj hydrogen bond analysis

From: Thomas Cheatham III (tec3_at_utah.edu)
Date: Wed Feb 18 2009 - 14:21:27 CST

> 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_at_O :100_at_N out d1.dat
distance hb2 :2_at_O :101_at_N out d2.dat
analyze statistics all

--tec3

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