Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions?

From: Thomas Cheatham <>
Date: Fri, 1 Dec 2006 10:53:50 -0700 (Mountain Standard Time)

On Fri, 1 Dec 2006, j j wrote:

> I trying to track some ions interactions by using the hbond facility in ptraj.
> To simplify input I've just wrote the essential commands to test:


> hbond

Note, you are better off specifying the series keyword to provide more
information ("series hbond1").

> (simplified). This seems to work fine: ptraj_test_OK.out

The standard default command uses a cutoff of 3 angstroms which works OK
for specifying water-donor or water-acceptor interactions. However, if
there is a water mediated interaction, interaction may not be found...

This is likely the case with Mg2+ which although having a small vdw radii
(using Aqvist parameters), it is usually hexa-hydrated. Therefore the
interaction with phosphate oxygen is

Mg-OH2 ... O?P-P

As the OW radii is 1.7 A (x2) > 3 angstroms. If you use,

hbond series h1 distance 3.5

you may see some interactions. In a longer trajectory, you may see direct
Mg2+ ... O?P interactions depending on whether the ion sheds water; this
may not be desirable as many Mg2+ interactions are water-mediated.

> In the A8 manual treats the case of ions interactions by specifying twice
> the atoms to probe. Page 211 [..]
> The acceptor command is similar except that both the heavy atom and the
> hydrogen atom are specified. If the same atom is specified twice (as might be the
> case to probe ion interactions) then no angle is calculated between the donor and
> acceptor.

> ==> <==
> trajin ions2test.trj.gz
> donor mask :1-76.O1P
> donor print
> #acceptor mask :77-86.MG :77-86.MG
> acceptor MG MG MG
> acceptor print
> hbond

Try "hbond series h1 out hbond.dat distance 3.5 angle -1.0"
or possibly even a larger cutoff (4.0).

You could also calculated the radial distribution function of the Mg2+
around the phosphate oxygens to see if there are any peaks (and at what

radial rdf_phosphate 0.1 10.0 .MG @O?P


The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Dec 03 2006 - 06:07:55 PST
Custom Search