Re: [AMBER] Question about mask in cpptraj

From: Mohd Farid Ismail <mohd.farid.ismail.yandex.com>
Date: Mon, 05 Oct 2015 12:19:05 +0800

   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>:

     On Sun, Oct 4, 2015 at 9:42 PM, Mohd Farid Ismail
     <[1]mohd.farid.ismail.yandex.com> 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
     (801) 585-6208 (Fax)

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References

   1. mailto:mohd.farid.ismail.yandex.com
   2. mailto:AMBER.ambermd.org
   3. http://lists.ambermd.org/mailman/listinfo/amber
   4. http://home.chpc.utah.edu/~cheatham/
   5. mailto:AMBER.ambermd.org
   6. http://lists.ambermd.org/mailman/listinfo/amber
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Received on Sun Oct 04 2015 - 21:30:03 PDT
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