[gmx-users] what\'s wrong with my dummy atom definition?

[nanyu101 at sina.com]

Dear gmx-users and Dr. Yang Ye
   
     I need to create a cationic dummy atoms for my zinc enzyme. I just do as Dr. Yang Ye and the mailing-list told. But the editconf and grompp do not recognize my dummy atom when I create a box and a tpr file. At the beginning, I just run pdb2gmx to create a protein topology file without the zinc cation. And then, I add the cationic dummy group to the end of gro file produced by the pdb2gmx. After doing this, I try to create a box for my whole system by editconf -bt cubic -f pro.gro -o pro_box.gro -p pro.top -c -d 1.0. In the pro_box.gro, the cationic dummy group was gone. The both gro file are listed here:

pro.gro (DZN is dummy group)
  184ARG    HD2 2879   3.932   1.483   3.431
  184ARG     NE 2880   3.834   1.338   3.332
  184ARG     HE 2881   3.747   1.380   3.360
  184ARG     CZ 2882   3.828   1.229   3.256
  184ARG    NH1 2883   3.940   1.169   3.217
  184ARG   HH11 2884   4.019   1.219   3.253
  184ARG   HH12 2885   3.917   1.090   3.161
  184ARG    NH2 2886   3.711   1.180   3.220
  184ARG   HH21 2887   3.637   1.236   3.258
  184ARG   HH22 2888   3.725   1.098   3.163
  184ARG      C 2889   4.340   1.577   3.248
  184ARG     O1 2890   4.428   1.679   3.229
  184ARG     O2 2891   4.344   1.456   3.187
  185DZN    DZ0 2893   17.682   8.854  32.262
  185DZN    DL1 2894   18.082   9.354  32.662
  185DZN    DL2 2895   17.682   8.854  33.162
  185DZN    DL3 2896   17.682   9.754  33.162
  185DZN    DL4 2897   18.582   8.854  33.162

the pro_box.gro (the dummy group does not exit)

  184ARG     CD 2877   3.957   1.402   3.379
  184ARG    HD1 2878   4.004   1.337   3.439
  184ARG    HD2 2879   3.932   1.483   3.431
  184ARG     NE 2880   3.834   1.338   3.332
  184ARG     HE 2881   3.747   1.380   3.360
  184ARG     CZ 2882   3.828   1.229   3.256
  184ARG    NH1 2883   3.940   1.169   3.217
  184ARG   HH11 2884   4.019   1.219   3.253
  184ARG   HH12 2885   3.917   1.090   3.161
  184ARG    NH2 2886   3.711   1.180   3.220
  184ARG   HH21 2887   3.637   1.236   3.258
  184ARG   HH22 2888   3.725   1.098   3.163
  184ARG      C 2889   4.340   1.577   3.248
  184ARG     O1 2890   4.428   1.679   3.229
  184ARG     O2 2891   4.344   1.456   3.187
   7.34890   7.34890   7.34890



Would you please give me some comments? Thank you very much.   
   
  My dummy atom type is listed here:  
   
   opls_966   DZ     65.37000     0.000       D    3.10000e-01  4.18200e-06  
   opls_967   DL      0.00000     0.500       D    0.00000e+00  0.00000e+00  
   
   
  And my itp file of dummy atoms is listed here.  
   
  [ moleculetype ]  
  ; molname       nrexcl  
  dzn             2  
   
  ; We use a strange order of atoms to make things go faster in GROMACS  
  [ atoms ]  
  ; id    at type res nr  residu name     at name         cg nr   charge  
     DZ0       opls_966     1       DZN              DZ             1       0.000  
     DL1       opls_967     1       DZN              DL             1       0.500  
     DL2       opls_967     1       DZN              DL             1       0.500  
     DL3       opls_967     1       DZN              DL             1       0.500  
     DL4       opls_967     1       DZN              DL             1       0.500  
   
  [ bonds ]  
    DZ0    DL1  
    DZ0    DL2  
    DZ0    DL3  
    DZ0    DL4  
   
  [ constraints ]  
  ; i     j       funct   distance  
  1       2       1       0.090000  
  1       3       1       0.090000  
  1       4       1       0.090000  
  1       5       1       0.090000  
   
  [ exclusions ]  
  1       2       3       4       5  
  2       1       3       4       5  
  3       1       2       4       5  
  4       1       2       3       5  
  5       1       2       3       4  
   
  [ dummies4 ]  
  ;     Dummy      from    funct       a        b        d  
  5    1    2     3     4    1         0.33333  0.33333 -0.105  
  1    2    3     4     5    1         0.33333  0.33333 -0.105  
  2    3    4     5     1    1         0.33333  0.33333 -0.105  
  3    4    5     1     2    1         0.33333  0.33333 -0.105  
  4    5    1     2     4    1         0.33333  0.33333 -0.105  



all your bests,
nanyu



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