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 <dur...@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 > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
