Re: [AMBER] finding number of atoms within a radius

From: Elvis Martis <>
Date: Wed, 24 May 2017 12:54:34 +0000

You can use radial distribution function (rdf).

Cpptraj command is as follows (paraphrasing from the Amber17 manual)

radial <outfilename> <spacing> <maximum> <solvent mask1> [<solute mask2>] [noimage] [density <density> | volume] [center1 | center2 | nointramol] [<name>] [intrdf <file>] [rawrdf <file>]
<outfilename> File to write RDF to, required.
<spacing> Bin spacing, required.
 <maximum> Max bin value, required.
  <solvent mask1> Atoms to calculate RDF for, required.
 [<solute mask2>] (Optional) If specified calculate RDF of all atoms in <solvent mask1> to each atom in <solute mask2>.
[noimage] Do not image distances.
[density <density>] Use density value of <density> for normalization (default 0.033456 molecules Å−3).
[volume] Determine density for normalization from average volume of input frames.
[center1] Calculate RDF from geometric center of atoms in <solvent mask1> to all atoms in <solute mask2>.
[center2] Calculate RDF from geometric center of atoms in <solute mask2> to all atoms in <solvent mask1>.
[nointramol] Ignore intra-molecular distances.
[<name>] Name radial dataset.
[intrdf <file>] Calculate integral of RDF bin values (averaged over # of frames but otherwise not normalized) and write to <file> (can be same as <output_filename>).
[rawrdf <file>] Write raw (non-normalized) RDF values to <file>.
DataSet Aspects:
[int] (intrdf only) Integral of RDF bin values.
[raw] (rawrdf only) Raw (non-normalized) RDF values.

Calculate the radial distribution function (RDF, aka pair correlation function) of atoms in <solvent mask1> (note
that this mask does not need to be solvent, but this nomenclature is used for clarity). If an optional second mask
(<solute mask2>) is given, calculate the RDF of ALL atoms in <solvent mask1> to EACH atom in <solute
mask2>. 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.

    Best Regards

Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy

A  Kalina, Santacruz [E], Mumbai 400098, INDIA
Skype. adrian_elvis12

-----Original Message-----
From: Debodyuti Dutta []
Sent: Wednesday, May 24, 2017 5:15 PM
Subject: [AMBER] finding number of atoms within a radius

Dear sir,
In my simulation I have a metal atom. Over the simulation, the number of water atoms around the metal change.
I want to calculate the number of water atoms within 6 angstrom radius of the metal in every frame.
How to do that with cpptraj?
thanks in advance

*Debodyuti Dutta*
Research Scholar
Indian Institute of Technology Kharagpur _______________________________________________
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Received on Wed May 24 2017 - 06:00:04 PDT
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