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

From: j j <fantvamp.gmail.com>
Date: Fri, 1 Dec 2006 21:28:24 +0100

 Dear Professor Cheatham,
Thank you very much for your detailed reply, hbond for MG works fine now.
( ptraj ions2test.prmtop < ptraj_cheatman_radial.in >
ptraj_cheatman_radial.stdout ) > & ptraj_cheatman_radial.sterr
Radial distribution gave me two outputs,
rdf_phosphate_volume.xmgr and rdf_phosphate_standard.xmgr,
should be also expected rdf_phosphate_carnal.xmgr?
Best regards,
JJ


2006/12/1, Thomas Cheatham <tec3.utah.edu>:
>
> 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:
>
> [chop]
>
> > 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.
>
> > ==> ptraj_names.in <==
> > 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
> distance).
>
> radial rdf_phosphate 0.1 10.0 .MG .O?P
>
> --tom
>
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Received on Sun Dec 03 2006 - 06:07:57 PST
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