Hi,
On Thu, Jan 31, 2013 at 10:27 PM, Marek Maly <marek.maly.ujep.cz> wrote:
> However, in the second command you are computing the RDF
>> of the geometric center (i.e. a single point) of the CEN residue(s) to
>> the atoms in every WAT residue.
>
> Here I don't agree with you. My interpretation of the second command is
> that
> according to the AT12 manual (page 189) here should be calculated RDF of
> WAT atoms to the geometric center of the CEN residuum (i.e. to the only
> one atom which exists in CEN res.)
The command functions exactly the way both you and I describe it. The
issue here is that I still think the RDF of:
radial out R1.agr .1 :WAT.O
and
radial out R1.agr :WAT.O .1
should not match. My reasoning is this: you can think of the RDF as
giving you the probability you will see something a certain distance
from something else, right?. In the first case I'm asking, "What's the
probability I see atom 1 a certain distance from any water oxygen?".
Since there are a lot of water oxygens but only 1 atom, the
probability I see atom 1 from any given water should be pretty low.
However, in the second case I'm asking, "What's the probability I see
a water oxygen a certain distance from atom 1". Since there are
presumably plenty of water residues (and assuming atom 1 is
solvent-exposed), the probability should be fairly near 1.
Hopefully this helps clear things up. The description of the 'radial'
command (among others) should definitely be clearer in the manual.
-Dan
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-9119 (Fax)
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Received on Fri Feb 01 2013 - 08:30:03 PST
