AMBER Archive (2006)
Subject: Re: AMBER: Ions analysis with hbond, How can I specify an input for hbond to probe ions interactions?
From: Thomas Cheatham (tec3_at_utah.edu)
Date: Fri Dec 01 2006 - 11:53:50 CST
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:
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
> ==> ptraj_names.in <==
> trajin ions2test.trj.gz
> donor mask :1-76_at_O1P
> donor print
> #acceptor mask :77-86_at_MG :77-86_at_MG
> acceptor MG MG MG
> acceptor print
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
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