[gmx-users] Parametrisation of the cyclic nucleotides in Gromos force fields

[James Starlight]

Dear Gromacs Users!


In one of my study I investigate interactions of the cyclic
nucleotides (cGMP and cAMP) with some cyclic-nucleotide-binding
proteins. I'm modelling that complexes in the gromos 56a7 ff with the
parameters for ligands made by prodrg.  So I'm not quite sure about
correctness of charge distributions of that cyclic nucleotides. E.g
below charges of my mollecule of cGMP (united atom modell) is present.


;   nr      type  resnr resid  atom  cgnr   charge     mass
     1         O     1  DRG      O6     7   -0.211  15.9994
     2         C     1  DRG      C6     7    0.211  12.0110
     3        NR     1  DRG      N1     8   -0.360  14.0067
     4         H     1  DRG      H1     8    0.360   1.0080
     5         C     1  DRG      C2     1    0.298  12.0110
     6        NT     1  DRG      N2     6   -0.830  14.0067
     7         H     1  DRG     H22     6    0.415   1.0080
     8         H     1  DRG     H21     6    0.415   1.0080
     9        NR     1  DRG      N3     1   -0.298  14.0067
    10         C     1  DRG      C4     2    0.210  12.0110
    11         C     1  DRG      C5     2    0.096  12.0110
    12        NR     1  DRG      N7     2   -0.626  14.0067
    13       CR1     1  DRG      C8     2   -0.030  12.0110
    14        HC     1  DRG      H8     2    0.006   1.0080
    15        NR     1  DRG      N9     2    0.179  14.0067
    16       CH1     1  DRG     C1*     2    0.165  13.0190
    17        OA     1  DRG     O4*     3   -0.176  15.9994
    18       CH1     1  DRG     C4*     3    0.240  13.0190
    19       CH1     1  DRG     C5*     3    0.089  14.0270
    20        OA     1  DRG     O5*     3   -0.177  15.9994
    21         P     1  DRG     PAQ     9    1.360  30.9738
    22        OA     1  DRG     OAR     9   -0.797  15.9994
    23        OM     1  DRG     OAS     9   -1.539  15.9994
    24        OA     1  DRG     O3*     4   -0.160  15.9994
    25       CH1     1  DRG     C3*     4    0.160  13.0190
    26       CH1     1  DRG     C2*     5    0.150  13.0190
    27        OA     1  DRG     O2*     5   -0.548  15.9994
    28         H     1  DRG     H8M     5    0.398   1.0080



Have anobody else modelled the same cyclic nucleotides in gromos ff ?
I'd like to compare my itp's of ligands with another works :)



James