Water outside protein surface

From: Pijush Ghosh (pijush.ghosh_at_ndsu.edu)
Date: Fri Sep 15 2006 - 00:06:39 CDT

Hello all

>From the previous discussion I found how to extract water molecules within
3.5 A of protein, that works fine. But I want only the water molecules say
4.0 A from outer surface of protein ( i.e outer peripheral water molecules
and not in the bulk). Can anybody suggest something?

One thing, had my protein been a globular one then perhaps I could have
considered it as a sphere and then selected those water molecules doing x>
something , x< something and y> something , y>something..but I have my
protein constantly changing in shape under SMD, that's why I am looking for
something general.


Appreciate your help,





Pijush Ghosh

PhD Student

Department of Civil Engineering

North Dakota State University

Fargo. ND. 58105. USA





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