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

[leafyoung81-group at yahoo.com]

--- nanyu101 at sina.com wrote:

> Dear gmx-users,
> 
>    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.
please attach (digested) error msg with the mail so
that we could know what happened. We cannot simply
reproduce what you had.

> 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
All you atoms are dummies. You got to have some real
atoms in the system.
> 
> [ 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
> ______________________________________
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