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

[James Starlight]

Justin,

Indeed the force field is the 54a7 ( modiffied version of the 54a6).

The main reason of using GROMOS ff in that case was the topology of
ligands which could be easily created by means of prodrg or ATB. On
other hand I've never worked with the protein-ligand complexes in
charmm ff for instance.

By the way is there any suitable builing blocks (implemented in the
rtp enties of the gromos ff) which could be used for charge
assignment?


James

2012/12/5 Justin Lemkul <jalemkul at vt.edu>:
>
>
> 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
>
> --
> ========================================
>
> 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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