Functional role of the internal water channel within the receptor

From: James Starlight (
Date: Tue Aug 08 2017 - 07:42:07 CDT

Dear VMD/NAMD users!

In my system, it is necessary to find how the density of internal
water changes as the distance from the active center of the protein.
Hence I am studying a functional role of the internal water on protein
dynamics via calculation of Radial Distribution function in VMD.

Here some of the questions:

1) how is better to determine the second sample of atoms (belongs to
active center of protein)? Is it better to use a single atom (for
example C-alpha) of specific residue, or averaged positions over the
coordinates of several atoms (for example, include all the amino acids
that form the inner cavity of the active site in the selection)?

2) What R max is reasonable for membrane receptor assuming that within
active site the amino-acids coordinate water within 2.7 A?

3) How dR should be defined? - by default it is 0.1 nm (thus being
equal to the diameter of the hydrogen atom). Should the dR be
increased, for example up to the order of the van der Waals radius of
the oxygen atom (which I select for water)?

Thanks you in advance!


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