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

[nanyu101 at sina.com]

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. 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
______________________________________
购惠普彩色全功能一体机送神奇四侠精美礼品( http://ad4.sina.com.cn/sina/limeng3/mail_zhuiyu/mail_zhuiyu_20051017.html )

===================================================================


注册新浪2G免费邮箱 (http://mail.sina.com.cn/chooseMode.html)