remarks param4.inp
remarks more tests for the atom and type-based parameters
remarks  Axel T. Brunger
remarks ==================================

topology reset @CNS_TOPPAR:protein-allhdg5-4.top end   {* this is the DG-version of this file *}

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

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

coor
ATOM      1  CA  TRP     1       1.331   1.246   0.096  1.00  0.00      TRYP
ATOM      2  HA  TRP     1       1.571   0.780   1.039  1.00  0.00      TRYP
ATOM      3  CB  TRP     1       2.535   2.085  -0.418  1.00  0.00      TRYP
ATOM      4  HB1 TRP     1       2.239   2.586  -1.319  1.00  0.00      TRYP
ATOM      5  HB2 TRP     1       2.751   2.850   0.315  1.00  0.00      TRYP
ATOM      6  CG  TRP     1       3.804   1.229  -0.669  1.00  0.00      TRYP
ATOM      7  CD1 TRP     1       4.717   0.866   0.299  1.00  0.00      TRYP
ATOM      8  HD1 TRP     1       4.659   1.099   1.355  1.00  0.00      TRYP
ATOM      9  CD2 TRP     1       4.351   0.653  -1.938  1.00  0.00      TRYP
ATOM     10  NE1 TRP     1       5.724   0.123  -0.275  1.00  0.00      TRYP
ATOM     11  HE1 TRP     1       6.486  -0.256   0.211  1.00  0.00      TRYP
ATOM     12  CE2 TRP     1       5.557  -0.035  -1.629  1.00  0.00      TRYP
ATOM     13  CE3 TRP     1       3.937   0.642  -3.303  1.00  0.00      TRYP
ATOM     14  HE3 TRP     1       3.030   1.139  -3.603  1.00  0.00      TRYP
ATOM     15  CZ2 TRP     1       6.307  -0.689  -2.607  1.00  0.00      TRYP
ATOM     16  HZ2 TRP     1       7.219  -1.201  -2.337  1.00  0.00      TRYP
ATOM     17  CZ3 TRP     1       4.699  -0.019  -4.279  1.00  0.00      TRYP
ATOM     18  HZ3 TRP     1       4.371  -0.014  -5.308  1.00  0.00      TRYP
ATOM     19  CH2 TRP     1       5.879  -0.680  -3.932  1.00  0.00      TRYP
ATOM     20  HH2 TRP     1       6.459  -1.186  -4.691  1.00  0.00      TRYP
ATOM     21  C   TRP     1       0.137   2.181   0.303  1.00  0.00      TRYP
ATOM     22  O   TRP     1      -0.629   2.346  -0.631  1.00  0.00      TRYP
ATOM     23  OXT TRP     1       0.010   2.715   1.393  1.00  0.00      TRYP
ATOM     24  N   TRP     1       0.945   0.198  -0.894  1.00  0.00      TRYP
ATOM     25  HT1 TRP     1       1.555  -0.635  -0.775  1.00  0.00      TRYP
ATOM     26  HT2 TRP     1      -0.048  -0.074  -0.740  1.00  0.00      TRYP
ATOM     27  HT3 TRP     1       1.057   0.571  -1.858  1.00  0.00      TRYP
END

energy end


parameter 
   reset 
   learn initialize selection=( all ) mode=nostatistics end
   learn accumulate end
   learn terminate end
   bonds ( all ) ( all ) 500. TOKEN
   angles ( all ) ( all ) ( all ) 200. TOKEN
   impropers ( all ) ( all ) ( all ) ( all ) 400. 0 TOKEN
   dihedrals ( all ) ( all ) ( all ) ( all ) 400. 0 TOKEN 
   nonbonded ( all )   0.1  1.0  0.1 1.0
   ?
end

energy end

parameter
   reset type
   reduce mode=statistics selection=( all ) end
   ?
end

do (segid=chemical) ( all )
do (chemical="C" ) ( name C* )
do (chemical="N" ) ( name N* )
do (chemical="O" ) ( name O* )
do (chemical="H" ) ( name H* )

parameter
   reset type   
   reduce mode=statistics selection=( all ) end
end

write parameter output=OUTPUT end

do (chemical=segid) ( all )
do ( segid="   " ) ( all )

parameter 
   reset type   
   reduce mode=average selection=( all ) end
   reset atom
   nonbonded ( all )   0.1  1.0  0.1 1.0
   ?
end

energy end

parameter
  reset
  ?
  reset all 
  ?
end

stop