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

[leafyoung81-group at yahoo.com]

--- ÎâÏÔ»Ô <nanyu101 at sina.com> wrote:

> Dear gmx-users and Dr. Yang Ye
>  
>      I need to create a cationic dummy atoms for my
> zinc enzyme. I just d=
> o as Dr. Yang Ye and the mailing-list told. But the
> editconf and grompp d=
> o 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 t=
> he zinc cation. And then, I add the cationic dummy
> group to the end of gr=
> o file produced by the pdb2gmx. After doing this, I
> try to create a box f=
> or 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. Th=
> e 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. 
This shall not be a problem with topology. Check no.
of atoms put to the second line in the gro file. I
guess that it is just 2891, excluding the dummy group.

Yang Ye