Re: [AMBER] request for help in radial command

From: Jason Swails <>
Date: Thu, 02 Jan 2014 09:04:06 -0500

On Thu, 2014-01-02 at 14:12 +0530, Robin Jain wrote:
> Dear sir,
> I want to calculate radial distribution function using cpptraj. I have a
> system of a organic molecule in 437 methanol. Now i want to know that

Everything you want to do is available _only_ with the latest version of
cpptraj. So make sure you have applied all of the updates to AmberTools
13 (if you are unsure, just configure and recompile AmberTools and Amber
if you have it; the configure script checks for updates and applies them
if you do not already have them). If any updates were downloaded, you
must recompile Amber for them to take effect.

> 1. how can i avoid intramolecular rdf calculation.

You need to use the "nointramol" keyword to the "radial" command in
cpptraj. This keyword is not specified in the AmberTools 13 manual, but
the rest of the keywords and command usage is.

> 2. how can i calculate rdf between solvent specify atom to solvent
> specifyatom.
> 3. how can i calculate rdf between solvent specify atom to solute specify
> atom.

This is easily accomplished simply by selecting the atoms you want
selected with the selection masks. The Amber mask syntax is described
in the Amber manual. Common selections are:

:<Residue> -- This selects a given residue (name or number is allowed)
.<Atom> -- This selects a given atom (name or number is allowed)

These can be combined with operators & (and), | (or), ! (not, unary
operator). For example:

:10 & .CA -- Selects the atom named CA in residue 10

The above is very common, and can be shortened to ':10.CA'.

You can use the ambmask program in Amber or either ParmEd or cpptraj to
experiment with different mask selection strings to get comfortable with
the syntax.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Jan 02 2014 - 06:30:02 PST
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