[AMBER] Distance restraint using com keyword

From: Sun <sunbintyy.163.com>
Date: Mon, 2 Sep 2013 22:27:50 +0800 (CST)

Dear All,
I want to define a distance restraint between COM( center of mass ) of two groups. I have checked the previous achive about this issue and amber manual. It seems that amber can only define the geometry center of a group when using iat(n) < 0 and igrn keyword to dedine the selection of atoms ( an example is as following )
  ixpk= 0, nxpk= 0, iat= -1,-1, r1= 1.30, r2= 1.80, r3= 2.90, r4= 3.40,
      rk2=20.0, rk3=20.0, ir6=1, ialtd=0
When this restraint file is uesd, the geoetry centers of the two group are selected . But what I actually want is the definition of COM of the two groups , hence I change the above file to this :
  ixpk= 0, nxpk= 0,
 rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
restraint = "distance( com(17,18) com(44,45) 2.9 )"

I submitted the mission using the new restraint file and everything seemd fine except for a warning message in the ouput file£º
 " Warning: More characters in restraint beyond final atom necessary
Using only first 2 atoms "
Could anyone give me some tips about what happend ?
Thanks very much !
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Received on Mon Sep 02 2013 - 07:30:03 PDT
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