AMBER Archive (2006)

Subject: AMBER: How to calculate RDF based on the center of mass of specific solute atoms?

From: Xioling Chuang (
Date: Sun Oct 15 2006 - 23:04:10 CDT

Dear All,

To calculate RDF from DNA atoms to water (oxygen atom) using command

    radial filename 0.05 8.5 :WAT_at_O :1-20 closest density 0.033456

as I understood, PTRAJ will calculate RDF based on DNA surface. My question
is that how to calculate the RDF based on center of mass of specific solute
atoms (e.g. center of mass of only residue 1)?
many thanks in advance for your suggestion.


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