> 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.O15
> acceptor mask :1-5.N6 :1-5.H118
> acceptor mask :1-5.N7 :1-5.H129
> acceptor mask :1-5.N4 :1-5.H79
> acceptor mask :1-5.N5 :1-5.H90
> acceptor mask :1-5.N2 :1-5.H40
> acceptor mask :1-5.N3 :1-5.H51
> acceptor mask :1-5.N :1-5.H
> acceptor mask :1-5.N1 :1-5.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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Received on Sun Dec 03 2006 - 06:07:55 PST
