[gmx-users] terminal phosphate residue for dna simulations

[Paulo Netz]

Hi Vedat

You are right. I think that a oligonucleotide with both 5' and 3' phophates
can be simulated,
but probably the charge density is too high (for instance a dodecamer would
carry a negative charge
of 26 instead of 22 in the regular definition or 24 if the 5' phosphates
are explicitly taken
into account). Anyway, the corresponding modifications would be
straightforward in
GROMACS files.

Best regards

Paulo Netz


On Thu, Feb 21, 2013 at 1:02 PM, Vedat Durmaz <durmaz at zib.de> wrote:

>
> hi paulo & gmx,
>
> thank you for your time and hint! as far as i've understood from your
> paper which was interesting to read, you mainly modelled 5'-phosphate
> molecules?
>
> anyways, since we intended to simulate a 3'-terminal phosphate as well, we
> just created a phosphate residue by modifying the file dna.rtp (and
> others). this residue can now be parameterized at any 3' as well as 5'
> terminus if desired.
>
> hopefully, this appoach is somehow valid and doesn't lead to strange
> artefacts.
>
> take care,
> vedat
>
> Am 19.02.2013 15:14, schrieb Paulo Netz:
>
>> Hi Vedat
>>
>> First of all, the coordinates input file (for instance, pdb) must have
>> terminal
>> nucleotides with "free", dangling phosphate groups. In most of the cases,
>> such terminal phosphates are absent. If the structure indeed has these
>> phosphates, it is possible to simulate a mono-, oligo- or polynucleotide
>> displaying these dangling phosphates with AMBER force field. You only
>> have to consider that the nucleotide definition of AMBER distinguishes
>> between the terminal nucleotides (normally without phosphate,
>> named for instance as DA3, DA5, DT3, DT5 etc.) and the regular nucleotides
>> (DA, DT, DC, DG). You just have to consider your terminal nucleotides
>> as regular ones (i.e. named as DA instead of DA3 or DA5 and so on).
>> More details you can find in my paper:
>>
>> doi: *10.1021*/*jp1035663*
>> *
>>
>> *
>> Best regards
>>
>> Paulo Netz
>>
>>
>> On Tue, Feb 19, 2013 at 10:35 AM, Vedat Durmaz <durmaz at zib.de> wrote:
>>
>>  hi guys,
>>>
>>> does anyone know about a way to simulate mono- or polynucleotides along
>>> with a 3' or 5' bound monophosphate using an amber force field like
>>> ffamber99sb?
>>>
>>> i couldn't find any residue definition for a terminal phosphate group
>>> such
>>> as " P3' " or " P5' " (exemplarily). do they indeed not exist or am i
>>> just
>>> not able to search them?
>>>
>>> thanks in advance & take care
>>> vedat
>>>
>>>
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