[gmx-users] Small molecule parametrization

[Sun Iba]

Hi
I have parametreized my small molecule with the help of ATB server. I have
learnt that ATB provides GROMOS charges better than PRODRG. However, I have
serious doubts regarding the charges assigned to hydrophobic groups. Also I
need to convert the calculated charges into GROMOS 43a1 set (force field I
am using). I am pasting the .itp file produced by ATB:

nr  type  resnr  resid  atom  cgnr  charge    mass    total_charge
    1   CH3    1    SCX1    C12    1    0.223  15.0350
    2    OE    1    SCX1     O1    1   -0.275  15.9994     ; -0.052
    3     C    1    SCX1     C3    2    0.476  12.0110
    4     C    1    SCX1     C2    2   -0.157  12.0110
    5     C    1    SCX1     C4    2   -0.376  12.0110
    6    HC    1    SCX1     H2    2    0.172   1.0080     ;  0.115
    7     C    1    SCX1     C6    3    0.095  12.0110
    8    HC    1    SCX1     H4    3    0.137   1.0080
    9     C    1    SCX1     C9    3   -0.386  12.0110
   10     C    1    SCX1    C13    3    0.478  12.0110
   11    NR    1    SCX1     N2    3   -0.525  14.0067     ; -0.201
   12     C    1    SCX1    C19    4    0.539  12.0110
   13    NR    1    SCX1     N4    4   -0.539  14.0067     ;  0.000
   14     C    1    SCX1     C1    5   -0.117  12.0110
   15    HC    1    SCX1     H1    5    0.157   1.0080
   16     C    1    SCX1     C5    5   -0.150  12.0110
   17    HC    1    SCX1     H3    5    0.131   1.0080     ;  0.021
   18     C    1    SCX1     C7    6    0.097  12.0110
   19     C    1    SCX1    C11    6    0.247  12.0110
   20    HC    1    SCX1     H6    6    0.079   1.0080
   21    NR    1    SCX1     N1    6   -0.423  14.0067     ;  0.000
   22    NT    1    SCX1     N3    7    0.171  14.0067
   23     C    1    SCX1    C16    7    0.387  12.0110
   24     O    1    SCX1     O2    7   -0.492  15.9994
   25     C    1    SCX1    C18    7    0.495  12.0110
   26     F    1    SCX1     F1    7   -0.187  18.9984
   27     F    1    SCX1     F2    7   -0.187  18.9984
   28     F    1    SCX1     F3    7   -0.187  18.9984     ;  0.000
   29     C    1    SCX1    C15    8   -0.211  12.0110
   30     C    1    SCX1    C14    8    0.388  12.0110
   31   CH3    1    SCX1    C10    8   -0.060  15.0350     ;  0.117
   32     C    1    SCX1    C22    9   -0.444  12.0110
   33    HC    1    SCX1    H11    9    0.187   1.0080
   34     C    1    SCX1    C21    9    0.309  12.0110
   35   CH3    1    SCX1     C8    9   -0.052  15.0350     ;  0.000
   36     C    1    SCX1    C20   10   -0.340  12.0110
   37    HC    1    SCX1    H10   10    0.226   1.0080
   38     C    1    SCX1    C17   10   -0.026  12.0110
   39    HC    1    SCX1     H8   10    0.140   1.0080     ;  0.000


Please have a look and help me understanding if the charges are too bad.
Also my Nitrogen atom is not aromatic. It is linked to C by triple bond and
to another N by double bond. Does GROMOS treat this type of nitrogn as NT
and NR?

Suniba