remarks dgtest4.inp
remarks   test the dg energy term
remarks    tests on an ALA polypeptide chain 
remarks Axel T. Brunger
remarks ==============

!---------------
! test one:  random four-atom metrization
!---------------


structure reset end
topology reset @CNS_TOPPAR:protein-allhdg5-4.top end

segment
   name="    "
   chain
      @CNS_TOPPAR:protein-allhdg5-4.link
      sequence ala ala ala ala ala 
               ala ala ala ala ala
      end
end
end

parameter 
        @CNS_TOPPAR:protein-allhdg5-4.param 
        nbonds repel = 0.8 end
end

set seed = 8787380 end

noe
   assign ( resid 1 and name ca ) ( resid 9 and name ca )  5. 0.01 0.01 
end

flags include noe end

mmdg
        iacc=0.2 tacc=0.2 bacc=0.001 pacc=0.2 
        writebounds=dgtest4.dat 
end
mmdg
        readbounds=dgtest4.dat
end

display $embedded
display $non_met_gap
display $dgscale

coor copy end

mmdg
        readbounds=dgtest4.dat
        storebounds
        selection=( all )
        scale=0.1   exponent=2
end

flags exclude * include dg end

test first selection= (  resid 9 and name ca ) 
   step=0.000001 tol=0.0 end

minimize powell nstep=200 drop=10. nprint=100  tolg=0. end

test first selection= ( resid 7 and name O  ) step=0.000001 tol=0.0 end

flags exclude * include bonds angles impr dihe vdw noe end
igroup interaction=( all )=( all ) weights * 0.0001 end end
energy end

coor swap end

mmdg
        readbounds=dgtest4.dat
        storebounds
        selection=( name ca or name n or name c )
        scale=0.1   exponent=2
end

flags exclude * include dg end

test first selection= (  resid 9 and name ca ) 
   step=0.000001 tol=0.0 end

minimize powell nstep=200 drop=10. nprint=100  tolg=0. end

test first selection= ( resid 7 and name O  ) step=0.000001 tol=0.0 end

flags exclude * include bonds angles impr dihe vdw noe end
igroup interaction=( name ca or name n or name c )=( prev ) 
           weights * 0.0001 end    end

energy end

stop