AMBER Archive (2006)

Subject: Re: AMBER: H-bond analysis (Ptraj) input file

From: Thomas Cheatham (tec3_at_utah.edu)
Date: Fri Dec 01 2006 - 11:56:57 CST

> I am trying to get information about H-bond in the system. When I use
> Ptraj to calculate, I found something that I don't understand.
> 1. For the acceptor, if I use mask, do I need to specify the heavy atom
> except the H atom?

You have specified it correctly, as below...

> 2. How to get a output file with all the H-bond information in it? I
> tried several time, but always failed.

Try replacing the "print" with the "series" keyword and give the series a
unique name, i.e.

> trajin md.mdcrd
> donor mask :1-5_at_O15
> acceptor mask :1-5_at_N6 :1-5_at_H118
> acceptor mask :1-5_at_N7 :1-5_at_H129
> acceptor mask :1-5_at_N4 :1-5_at_H79
> acceptor mask :1-5_at_N5 :1-5_at_H90
> acceptor mask :1-5_at_N2 :1-5_at_H40
> acceptor mask :1-5_at_N3 :1-5_at_H51
> acceptor mask :1-5_at_N :1-5_at_H
> acceptor mask :1-5_at_N1 :1-5_at_H11
>
> donor print
> acceptor print
>
> hbond print 0.05 out output_hbond2.dat

hbond series h1 out output_hbond2.dat

--tom

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