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 <[email protected]> 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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