AMBER Archive (2006)

Subject: Re: AMBER: RDF calculation

From: Thomas Cheatham (
Date: Tue Oct 17 2006 - 10:23:05 CDT

> Can PTRAJ calculate RDF of water to center of mass of solute atoms? If yes,
> what command should be used?

At present, no it cannot. Either all solute-solvent distances or the
closest solute-to-solvent distances are binned. The code could be
modified to do this (transformRadial() in actions.c). However, in the
absence of code modifications, I would suggest picking the atom closest to
the center of mass. Note however that the RDF around a solute may not
provide much useful information unless the solute is spherical (depending
of course on what you are trying to see). I normally find that picking
key surface residues and looking at RDF's to these is more meaningful
(especially when combined with further analysis, such as grids of solvent
density and hbond analysis to water).


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