Re: [AMBER] Correctly defining keywords in cpptraj - radial

From: Daniel Roe <>
Date: Thu, 13 Oct 2016 08:41:15 -0400

On Wed, Oct 12, 2016 at 6:45 PM, Stregone <> wrote:
> confirm that my script is correct, cause I am getting some estrange results. Unfortunately, I did not find answer in the AMBER mail list regarding to my issue.
> # script
> parm prmtop
> trajin mdcrd
> radial r.rdf 0.1 15 :1 :DBR volume center1
> (this is for calculating the rdf from the residue 1[mask1] to any DBR [mask2] residue)

When calculating the RDF the order in which you specify masks matters.
In general, you want the first mask to be the one containing more
entities, so in this case you probably want the order to be ':DBR :1'
(see the manual for further details).

> radial ra.rdf 0.1 15 :1.C:DBR volume
> (if I understood correctly, this is for finding from the C atom in the residue 1, atom that belong to DBR residue)

Looks like you might be missing a space between ':1.C' and :DBR (as it
is it is not a valid mask). Also, as above, you probably want ':DBR

> radial radi.rdf 0.1 15 :1:DBR volume center1

Again, you need a space between :1 and :DBR. In that case it is the
same as the first command.

Hope this helps,


Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Thu Oct 13 2016 - 06:00:04 PDT
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