Re: [AMBER] RDF 3 files and 3 columns

From: Thomas Cheatham III <>
Date: Mon, 26 Jul 2010 16:49:24 -0600 (Mountain Daylight Time)

> I used ptraj for this. I have got 3 .xmgr files generated: volume, standard and
> carnal.

"carnal" is for backward compatibility. Volume uses the system volume to
normalize, whereas the "standard" uses the density to normalize.
Essentially, you want the RDF to go to unity (1.0) at longer distances (of
course this may not occur in small boxes since periodic imaging is not
currently performed).

> I looked up in the manual amber9, and in the mailing list but I cannot find the
> meaning of the 3 columns in each file. I am interested in plotting the radial

distance RDF-value integral

> density distribution of water HOH inside my macromolecule versus R.
> I want to use the center of mass of the macromolecule as the reference. I
> performed explicit solvent MD.

There is not code implemented to do this at present; it would not be so
difficult to modify the code to allow calculation of the RDF relative to
the origin (where the molecule could be centered).

I had not thought of tracking water inside a molecule, however I actually
have a need to do this in some older work.

As written the code will only do the RDF to a specific atom, to all the
atoms at once, or to only the atom in a mask that is closest to the water.

If you do not want to edit the code, an approximate way to do this,
assuming the core is not particularly mobile:

 (1) center the molecule to the origin
 (2) create a pdb file

trajin pdb_bond_wat_md1_exp.mdcrd 1 1 1
trajout vis.pdb pdb
center :1-121 mass origin

 (3) add a dummy ATOM entry at the origin to the PDB

Add a line to the bottom of the PDB such as:

ATOM 0 X XXX 0 0.000 0.000 0.000

 (4) visualize to find the atom that is closest to this dummy atom .X

let's assume it is :43.CA

 (5) calculate the RDF around this atom.
trajin pdb_bond_wat_md1_exp.mdcrd
trajin pdb_bond_wat_md2_exp.mdcrd
center :1-121 mass origin
image origin center familiar
radial pdb_bond_wat_rad_dens.rdf 0.5 40.0 :WAT :43.CA

I'll think about adding the options for "origin" (since when combined with
the center command does the COM implicitly).


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Received on Mon Jul 26 2010 - 16:00:04 PDT
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