AMBER Archive (2006)

Subject: AMBER: RDF output

From: Jardas sucuriba (
Date: Tue Aug 29 2006 - 09:48:29 CDT


I have tried to calculate the radial distribution functions for specific
residues with water and I have some questions related with the output:

1) The amber 8 manual says that three files are produced, but I didnīt
obtain the file corresponding to the carnal style RDF. Does anyone know why?

2) The rdf values that come in the second column of the volume.xmgr file are
all zero but the standard.xmgr file contains the "normal/expected" values.
Is this correct? What the difference in the values that should I obtain?

My input file is:

trajin md2_1.mdcrd.gz
trajin md2_2.mdcrd.gz
center origin :1-256
image origin center familiar
radial C8rdf_O.05_8.xmgr 0.05 8.0 :WAT_at_O :256_at_C8
radial N11rdf_O.05_8.xmgr 0.05 8.0 :WAT_at_O :256_at_N11


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