[gmx-users] Ligand Topology file

[neha bharti]

Hello All

I am performing Molecular dynamics simulation of protein and ligand
complex. I am using GROMOS96 53a6 force field. For Ligand topology file I
am using Automated topology builder.
In the grompp step ( grompp -f ion.mdp -c solv.gro -p topol.top -o
ions.tpr) when I tried to add ion it gives me Note that

NOTE 2 [file topol.top]:
  The largest charge group contains 14 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.


Following is the atom charge group of .itp file which I get from Automated
topology builder



[ atoms ]
;  nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
    1     C           1    6P5P    C15    1   -0.050  12.0110
    2     C           1    6P5P    C16    1    0.023  12.0110
    3     C           1    6P5P    C17    1    0.023  12.0110
    4     C           1    6P5P    C18    1   -0.050  12.0110
    5     C           1    6P5P    C19    1    0.023  12.0110
    6     C           1    6P5P    C20    1    0.023  12.0110
    7     C           1    6P5P    C14    1    0.580  12.0110
    8     O           1    6P5P     O1     1   -0.571  15.9994
    9     C           1    6P5P    C21    1    0.570  12.0110
   10     O          1    6P5P     O2    1   -0.571  15.9994      ;  0.000
   11     N          1    6P5P     N3    2   -0.486  14.0067
   12     H          1    6P5P    H11    2    0.486   1.0080      ;  0.000
   13     C          1    6P5P    C12    3    0.251  12.0110
   14     C          1    6P5P    C11    3   -0.019  12.0110
   15     C          1    6P5P    C10    3   -0.070  12.0110
   16     C          1    6P5P     C9    3    0.089  12.0110
   17     C          1    6P5P     C8    3   -0.185  12.0110
   18     C          1    6P5P    C13    3   -0.089  12.0110
   19     C          1    6P5P     C7    3    0.491  12.0110
   20    NR        1    6P5P     N2    3   -0.468  14.0067      ; -0.000
   21    NR        1    6P5P     N1    4   -0.365  14.0067
   22     H          1    6P5P     H1    4    0.365   1.0080      ;  0.000
   23     C          1    6P5P     C5    5    0.155  12.0110
   24     C          1    6P5P     C4    5    0.115  12.0110
   25     C          1    6P5P     C6    5   -0.042  12.0110
   26     C          1    6P5P     C3    5   -0.042  12.0110
   27     C          1    6P5P     C2    5   -0.093  12.0110
   28     C          1    6P5P     C1    5   -0.093  12.0110      ;  0.000
   29     N          1    6P5P     N4    6   -0.486  14.0067
   30     H          1    6P5P    H16    6    0.486   1.0080      ;  0.000
   31     C          1    6P5P    C22    7    0.240  12.0110
   32     C          1    6P5P    C27    7   -0.100  12.0110
   33     C          1    6P5P    C26    7   -0.196  12.0110
   34     C          1    6P5P    C25    7    0.078  12.0110
   35     C          1    6P5P    C24    7   -0.081  12.0110
   36     C          1    6P5P    C23    7   -0.030  12.0110
   37     C          1    6P5P    C28    7    0.478  12.0110
   38    NR        1    6P5P     N6    7   -0.475  14.0067
   39     C          1    6P5P    C34    7    0.138  12.0110
   40     C          1    6P5P    C29    7    0.170  12.0110
   41     C          1    6P5P    C33    7   -0.030  12.0110
   42     C          1    6P5P    C30    7   -0.030  12.0110
   43     C          1    6P5P    C31    7   -0.081  12.0110
   44     C          1    6P5P    C32    7   -0.081  12.0110      ;  0.000
   45    NR        1    6P5P     N5    8   -0.365  14.0067
   46     H          1    6P5P     H2    8    0.365   1.0080      ;  0.000
; total charge of the molecule:  -0.000



Should I ignore the error or is there something wrong in my charge group
generated from ATB.
Can any one please help me out to solve the problem.

Thanks You.

With Regards
Neha Bharti