Re: AMBER: example script for hbond calculation

From: Thomas E. Cheatham, III <>
Date: Fri, 1 Jul 2005 10:10:07 -0600 (Mountain Daylight Time)

> Date: Thu, 30 Jun 2005 07:27:15 +0100 (BST)
> From: Vijay Manickam Achari <>
> trajin micelwat_md16_20.mdcrd
> prnlev 2
> #donor mask :1-27.O2',O3',O4',O5',O6'
> donor mask :1-27.O2'
> donor mask :1-27.O3'
> donor mask :1-27.O4'
> donor mask :1-27.O5'
> donor mask :1-27.O6'
> acceptor mask :1-27.O4 :1-27.H8
> acceptor mask :1-27.O3 :1-27.H9
> acceptor mask :1-27.O2 :1-27.H10
> acceptor mask :1-27.O6 :1-27.H11
> donor print
> acceptor print
> prnlev 0
> hbond out output_hb2.dat \
> time 1.0 \
> angle 120.0 \
> distance 4.0
> ---------------------------------------------
> My question:
> 1) what is the meaning of apostrophy (') every end of
> atom name in donor line?

The apostrophe is there since you are trying to match donors with atom
names O2', O3', ...

> 2) is there any different in writing the donor atoms
> horizontal way or vertical way..?

I have no idea what you mean here; each donor command needs to be on a
single line, but it is possible to specify as many donors (donor commands)
as you want (subject to memory limitations).

> 3) in acceptor line do i need to put the symbol (')
> end of Oxygen atom??

If your oxygen atom has ' in its name then yes, if it does not have ' in
its name than no.

Since you are obviously confused, let me try to explain it a bit better.
However, I will remind all that a good way to try to figure things out is
to actually run the commands and see what happens...

Let's say you have molecules as follows (were I am showing the atom

       H12 H2 O3
        | | ||

....and you are interested in probing hydrogen bonds between these
molecules in solution, in particular

   N2-H2 --- O3
   N2-H2 --- O4
   N2-H2 --- N2

You would specify a list of possible electron pair donors:

donor mask .O3
donor mask .O4
donor mask .N2

And a list of possible electron pair acceptors (which represents two atoms

acceptor mask .N2 @H2

Those commands, acceptor and donor, simply set up a list of possible
interaction pairs. The actual work is done by the next command:

  hbond out output_hb2.dat \
          time 1.0 \
          angle 120.0 \
          distance 4.0

The time is time/per frame in ps, so 1.0 means that each snapshot in the
trajectory you are studying is 1 ps apart. The distance cutoff is
specified above as 4.0 angstroms (which may be a bit long since h-bonds
are normally ~3.1 A heavy atom to heavy atom; I often use a cutoff of 3.5
A). For more information, you want to specify the "series" keyword.

   hbond series out output_hb2.dat time 1.0 angle 120.0 distance 3.5

If you search the archives, I have previous e-mails that describe how to
interpret the output.

Try it out first on a short trajectory, read the complete ptraj manual to
understand masks and atom selection and good luck...

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Received on Fri Jul 01 2005 - 17:53:01 PDT
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