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

From: Daniel Roe <>
Date: Fri, 14 Oct 2016 09:41:08 -0400

On Fri, Oct 14, 2016 at 8:19 AM, Stregone <> wrote:
> radial CH3CN_N1 .1 15.0 :ACN.N
> Or that this mean that it will calculate the RDF for the mask :ACN.N to any molecule around ??

It will be from all N atoms in residues named ACN to each other. I
suggest reading the Amber 16 manual entry for cpptraj radial (29.9.57,
page 606) if you are going to be using this command.

> I did calculate the RDF as you suggested " :DBR :1 ", unfortunately. I got something quite strange
> #Distance_(Ang) :1_=>_:DBR

It seems that you actually used ":1 :DBR" (at least for the output you
give) since when cpptraj outputs radial data the legend order matches
the order of the masks.

> I assume that because I am studying a solvent, I must be more careful with the mask.
> therefore I did try :1.C :DBR.C, which gave me more "natural" results.
> #Distance_(Ang) :1.C_=>_:DBR.C

Note how in this output the order of the masks in the legend matches
the order of the masks you gave.

> Any advise that I should follow?
> Also, how do I save the average density of the calculations ?

Not sure what you mean by average density here. Output for 'radial' is
controlled by several keywords. Please read the manual entry for
'radial' in it's entirety.


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 Fri Oct 14 2016 - 07:00:02 PDT
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