[gmx-users] can anyone give me a copy of dummy atom itp file?

[吴显辉]

Dear gmx-users,

        I am trying to create a dummy atom itp file for my cationic dummy force field file for my zinc enzyme, but I do fail in create a right itp file. I read the manual, the information is very compact. So I hope one of you can give me a hand. By the way, how to add the exclusion and constraints for the dummy atoms?
thank you.

the itp file I created 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
   1       opls_966     1       DZN          DZ0             1       0.000
   2       opls_967     1       DZN          DL1             1       0.500
   3       opls_967     1       DZN          DL2             1       0.500
   4       opls_967     1       DZN          DL3             1       0.500
   5       opls_967     1       DZN          DL4             1       0.500

[ bonds ]
    2892  2893     1
    2892  2894     1
    2892  2895     1            
    2892  2896     1
       
[ angles ]
 2893  2892  2894     1
 2893  2892  2895     1            
 2893  2892  2896     1
 2894  2892  2895     1
 2894  2892  2896     1
 2895  2892  2896     1

[ dummies4 ]
;     Dummy      from    funct       a        b        d
5    1    2     3     4    1         0.33333  0.33333 -0.105
[ dummies4 ]
1    2    3     4     5    1         0.33333  0.33333 -0.105
[ dummies4 ]
2    3    4     5     1    1         0.33333  0.33333 -0.105
[ dummies4 ]
3    4    5     1     2    1         0.33333  0.33333 -0.105
[ dummies4 ]
4    5    1     2     3    1         0.33333  0.33333 -0.105
------------------------------------------

thank you

all your bests
nanyu
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