AMBER Archive (2006)

Subject: AMBER: Picking up water molecules around one molecule

From: Atsutoshi Okabe (okabe_at_cherry.bio.titech.ac.jp)
Date: Sat Sep 23 2006 - 03:26:12 CDT

Dear all,

I want to calculate translational diffusion coefficients of water around 3.5
$B"r(B distance of oxygen atoms of one solute molecule(

such as one saccharide) and of water in bulk.

I guess that I can calculate it using the diffusion command of Ptraj with
Amber8.

But I don$B!G(Bt know how to pick up water molecules around arbitrary distance
from a solute molecule .

Can I do it within Amber program ?

Does anyone give me any suggestions ?

Thanks

Atsutoshi

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