>< 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 ??
>I t 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.
By the moment I only have access to amber tools 14. But I already had read the instructions (28.10.39 - 541),
but as I mentioned it is the fist time using this command.
So for example, I could use the command nointramol if in my case,
I have several atom with the same name in the input molecule???
>< 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 did use :1 :DBR, cause when I used " :DBR :1" it gave me a file with 0, all the values were "0".
>< 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.
Sorry, mia culpa. I meant the there is a key word "volume", it calculate the average density over the frames,
I would like to keep that value somewhere in the file . That is what I did mean.
-Dan
-------- Original Message --------
Subject: Re: [AMBER] Correctly defining keywords in cpptraj - radial
Local Time: October 14, 2016 1:41 PM
UTC Time: October 14, 2016 1:41 PM
From: daniel.r.roe.gmail.com
To: AMBER Mailing List <amber.ambermd.org>
On Fri, Oct 14, 2016 at 8:19 AM, Stregone <stregone.protonmail.com> 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.
-Dan
--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Oct 14 2016 - 07:30:02 PDT
