Yes that works for water. Sometimes I want to get the RDF of other bigger
solvent, for example cyclohexanone. I've been using an atom in the molecule
asyou suggested as a workaround.
--
Mohd Farid Ismail
05.10.2015, 21:02, "Daniel Roe" <daniel.r.roe.gmail.com>:
Why not use
radial file1.dat :WAT.O :SOLUTE volume center2 intrdf file1.dat
instead since the vdW radius of the water oxygen encloses the hydrogens
anyway?
-Dan
On Sunday, October 4, 2015, Mohd Farid Ismail
<[1]mohd.farid.ismail.yandex.com>
wrote:
Thank you Dr. Roe. Is there a way to do rdf between center of masses?
For
example, if I want the RDF of center of geometry of water around the
center
of geometry of my solute mask2, is there a way to do this?
I tried
radial file1.dat :WAT :SOLUTE volume center1 center2 intrdf file1.dat
but the output mentioned error or warning that only one center1 or
center2
is allowed.
--
Mohd Farid Ismail
05.10.2015, 11:54, "Daniel Roe" <[2]daniel.r.roe.gmail.com <javascript:;>
>:
On Sun, Oct 4, 2015 at 9:42 PM, Mohd Farid Ismail
<[1][3]mohd.farid.ismail.yandex.com <javascript:;>> wrote:
radial file1.dat 0.1 20 .C1 :200 volume intrdf file1.dat
where residue 200 is a 10-atom solvent molecule, does this calculates
the
RDF from the center of geometry of residue 200?
No, by default it uses every atom in the mask. To use the center of
the atoms in the mask use the 'center2' keyword (since it is the
second mask - you would use 'center1' if you wanted the center of the
first mask).
-Dan
--
Mohd Farid Ismail
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University of Utah
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Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
[17]
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(801) 587-9652
(801) 585-6208 (Fax)
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http://lists.ambermd.org/mailman/listinfo/amber
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http://home.chpc.utah.edu/~cheatham/
13. mailto:AMBER.ambermd.org
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17.
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Received on Mon Oct 05 2015 - 22:30:02 PDT
