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

[Justin Lemkul]

On 12/5/12 12:57 PM, James Starlight wrote:
> 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 ?

Is there any particular reason you're using Gromos96 instead of say, AMBER or 
CHARMM?  The latter perform significantly better than Gromos.

> I'd like to compare my itp's of ligands with another works :)
>

At quick glance and without knowing what the ligand you've shown actually is, 
the charges look reasonable for the 43A1 parameter set, but I don't know which 
you're trying to actually use - 56A7 doesn't exist as far as I know.  Do you 
mean 53A6 or 54A7?  If so, the charges do not seem right.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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