Hi ,
you're right, sorry I didn't see it. However have a look to this options
from Amber Manual :
"
radial <outfilename> <spacing> <maximum> <solvent mask1>
[<solute mask2>] [noimage] [density <density> | volume]
[center1 | center2 | nointramol] [<name>]
[intrdf <file>] [rawrdf <file>]
If desired, the geometric center of atoms in <solvent mask1> or <solute
mask2> can be used by
specifying the center1 or center2 keywords respectively, or alternatively
intra-molecular distances can be ignored
by specifying the nointramol keyword. "
So, this means that you should be specifying the center mass of your target
and type it in the space "centerx" .
I hope to have been helpuful.
Cheers,
Emanuele
2018-06-25 11:37 GMT+01:00 Shilpa Gupta <guptashilpa0605.gmail.com>:
> Hello Emanuele,
>
> Thanks for the reply. In the provided link rdf may be calculated using
> specific atom of a residue ,i.e., ACN.N but i want to calculate
> distribution around center of mass of a solute.
>
> On 25 June 2018 at 15:59, emanuele falbo <falbo.emanuele.gmail.com> wrote:
>
> > Dear ,
> >
> > follow this link , which explains well how to proceed :
> >
> > http://ambermd.org/tutorials/advanced/tutorial15/Tutorial2.xhtml
> >
> > Cheers,
> > Emanuele
> >
> > Il 25 giu 2018 10:58, "Shilpa Gupta" <guptashilpa0605.gmail.com> ha
> > scritto:
> >
> > > Dear Amber Users,
> > > I have a system in which solute is solvated by water. How can i
> calculate
> > > distribution of water molecules around solute using cpptraj,
> considering
> > > the center of mass of the solute?
> > >
> > >
> > >
> > >
> > > From
> > > Shilpa Gupta
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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Received on Mon Jun 25 2018 - 04:00:02 PDT
