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 <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" <daniel.r.roe.gmail.com <javascript:;>
> >:
>
> On Sun, Oct 4, 2015 at 9:42 PM, Mohd Farid Ismail
> <[1]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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> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 307
> Salt Lake City, UT 84112-5820
> [4]http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
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> References
>
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> 2. mailto:AMBER.ambermd.org <javascript:;>
> 3. http://lists.ambermd.org/mailman/listinfo/amber
> 4. http://home.chpc.utah.edu/~cheatham/
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--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Oct 05 2015 - 06:30:03 PDT
