[gmx-users] terminal phosphate residue for dna simulations

Paulo Netz paulo.netz at gmail.com
Tue Feb 19 15:14:07 CET 2013

Hi Vedat

First of all, the coordinates input file (for instance, pdb) must have
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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