[gmx-users] Partial atomic charge

[parto haghighi]

Dear GMX users,

I could make topology file of a ligand molecule by PRODRG but it has wrong
charge on each atom and as mentioned in Gromacs tutorial (protein-ligand
complex) I have used quantum mechanic calculation (like spartan) to correct
its charge:

.itp file from PRODRG:

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CH3     1  DRG     CAA     1    0.092  15.0350
     2       CH2     1  DRG      CAI     1    0.107  14.0270
     3         NL     1  DRG         N     1    0.702  14.0067
     4           H     1  DRG         H     1   -0.007   1.0080
     5       CH2     1  DRG     CAJ     1    0.106  14.0270
     6       CH3     1  DRG     CAB     2    0.071  15.0350
     7       CH2     1  DRG       CA     2    0.089  14.0270
     8           C     1  DRG         C     2    0.343  12.0110
     9           O     1  DRG         O     2   -0.733  15.9994
    10           N     1  DRG     NAL     2    0.120  14.0067
    11           H     1  DRG     HKL     2   -0.009   1.0080
    12           C     1  DRG     CAP     2    0.119  12.0110
    13           C     1  DRG     CAN     3   -0.037  12.0110
    14       CH3     1  DRG     CAC     3    0.047  15.0350
    15       CR1     1  DRG     CAG     3   -0.020  12.0110
    16         HC     1  DRG     HAN     3    0.013   1.0080
    17       CR1     1  DRG     CAF     3   -0.020  12.0110
    18        HC      1  DRG     HAM    3    0.013   1.0080
    19       CR1     1  DRG     CAH     3   -0.020  12.0110
    20         HC     1  DRG     HAO     3    0.013   1.0080
    21           C     1  DRG     CAO     3   -0.036  12.0110
    22       CH3     1  DRG     CAD     3    0.047  15.0350




.itp file whit modification based on Hatree-Fock quantum chemical
calculations using 6-31* basis set:


;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CH3     1  DRG     CAA     1    -0.507    15.0350
     2       CH2     1  DRG      CAI     1    0.117     14.0270
     3         NL     1  DRG          N     1    0.372    14.0067
     4           H     1  DRG          H     1    0.391      1.0080
     5       CH2     1  DRG      CAJ     1    0.104    14.0270
     6       CH3     1  DRG      CAB     2    -0.512   15.0350
     7       CH2     1  DRG        CA     2    -0.368   14.0270
     8           C     1  DRG          C     2    0.983   12.0110
     9           O     1  DRG          O     2    -0.656   15.9994
    10          N     1  DRG      NAL     2    -0.689   14.0067
    11          H     1  DRG      HKL     2    0.391       1.0080
    12          C     1  DRG      CAP     2    -0.105   12.0110
    13          C     1  DRG      CAN     3     0.367   12.0110
    14       CH3     1  DRG     CAC     3    -0.700    15.0350
    15       CR1     1  DRG     CAG     3   -0.364    12.0110
    16         HC     1  DRG     HAN     3    0.189     1.0080
    17       CR1     1  DRG      CAF     3   -0.079    12.0110
    18         HC     1  DRG     HAM     3    0.159    1.0080
    19        CR1     1  DRG     CAH     3   -0.412   12.0110
    20         HC     1  DRG     HAO     3    0.202    1.0080
    21           C     1  DRG     CAO     3   0.425  12.0110
    22       CH3     1  DRG     CAD     3    -0.739  15.0350



.itp file of a reference (dynamic and structural properties of lidocaine in
lipid bilayer,Carl-Johan Högberg, Arnold Maliniak, Alexander P. Lyubartsev
⁎ http://www.elsevier.com/locate/biophyschem ):

[ atoms ]
;   nr      type  resnr resid  atom  cgnr   charge     mass
     1       CH3     1  DRG     CAA     1    0.025    15.0350
     2       CH2     1  DRG      CAI     1    0.248    14.0270
     3         NL     1  DRG         N     1    0.049    14.0067
     4           H     1  DRG         H     1    0.405     1.0080
     5       CH2     1  DRG     CAJ     1    0.248    14.0270
     6       CH3     1  DRG     CAB     2    0.025    15.0350
     7       CH2     1  DRG       CA     2    0.000    14.0270
     8           C     1  DRG         C     2    0.227    12.0110
     9           O     1  DRG         O     2   -0.411    15.9994
    10           N     1  DRG     NAL     2    0.088    14.0067
    11           H     1  DRG     HKL     2   0.008    1.0080
    12           C     1  DRG     CAP     2    0.088   12.0110
    13           C     1  DRG     CAN     3   -0.004   12.0110
    14       CH3     1  DRG     CAC     3    0.030   15.0350
    15       CR1     1  DRG     CAG    3   -0.013   12.0110
    16        HC     1  DRG     HAN     3               1.0080
    17       CR1     1  DRG     CAF     3   -0.013   12.0110
    18         HC     1  DRG     HAM     3               1.0080
    19       CR1     1  DRG     CAH     3   -0.013   12.0110
    20         HC     1  DRG     HAO     3               1.0080
    21           C     1  DRG     CAO     3    -0.005 12.0110
    22       CH3     1  DRG     CAD     3    0.022  15.0350

I have tried all of them several times but they are very different from
each other.
What can I do? and when I use for example spartan to calculate charges how
can I select which one of methods are the best ? what is the reliable
reference to compare my result with?

Thanks a lot in advance.
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