You'll have to do it manually. Perhaps VMD or Chimera can help you with adding the atoms to the initial pdb. Then you'll have to create a modified amino acid topology for the amino acid that is getting phosphorylated in your forcefield's .rtp file.
On 2012-09-03 10:05:08AM +0200, reising...@rostlab.informatik.tu-muenchen.de wrote: > I want to add the phosphor first. > And I hoped that there is a program just like the "pdb2gmx" which adds > hydrogens to the protein. > > > You haven't anwsered my question. Did you just want to add the phosphate > > before starting the simulation or were you hoping for the simulation to do > > it > > for you? > > > > > > On 2012-09-03 09:51:12AM +0200, > > reising...@rostlab.informatik.tu-muenchen.de wrote: > >> Hi, > >> I have my protein without phosphorylations and now I want to > >> phosphorylate > >> one residue of my protein. > >> Is this possible? > >> > >> Thank you > >> > >> > can you be a bit more specific? Are you expecting to phosphorylate the > >> > protein along the trajectory or did you want to run continuous > >> simulations > >> > with different phosphorylation states? > >> > > >> > > >> > On 2012-09-03 09:30:58AM +0200, > >> > reising...@rostlab.informatik.tu-muenchen.de wrote: > >> >> Hi everybody, > >> >> > >> >> I want to add a phosphate to my protein. Is this possible with > >> gromacs? > >> >> > >> >> Thank you > >> >> > >> >> -- > >> >> 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 > >> > > >> > -- > >> > ================================================================== > >> > Peter C. Lai | University of Alabama-Birmingham > >> > Programmer/Analyst | KAUL 752A > >> > Genetics, Div. of Research | 705 South 20th Street > >> > p...@uab.edu | Birmingham AL 35294-4461 > >> > (205) 690-0808 | > >> > ================================================================== > >> > > >> > -- > >> > 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 > >> > > >> > >> > >> -- > >> 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 > > > > -- > > ================================================================== > > Peter C. Lai | University of Alabama-Birmingham > > Programmer/Analyst | KAUL 752A > > Genetics, Div. of Research | 705 South 20th Street > > p...@uab.edu | Birmingham AL 35294-4461 > > (205) 690-0808 | > > ================================================================== > > > > -- > > 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 > > > > > -- > 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 -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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