Re: [AMBER] RDF 3 files and 3 columns

From: Thomas Cheatham <>
Date: Thu, 29 Jul 2010 19:44:56 -0600 (Mountain Daylight Time)

> all volume and standard files give me RDF=0, only carnal has got some non zero

Perhaps your solute has a radius > 20A and there is no water inside? As a
first check, do the RDF of the water only. If this doesn't look
"normal" something funny is happending. If this looks good then do the
RDF to a surface residue... Try to experiment; also drop snapshots for
visualization to make sure things look OK. Note that if there is only a
few waters inside the solute, this will show as values close to zero. As
your radius expands, the ratio to bulk decreases rapidly!

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Received on Thu Jul 29 2010 - 19:00:03 PDT
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