[gmx-users] Adding phosphate to protein

[Peter C. Lai]

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, reisingere at 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,
> > reisingere at 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,
> >> > reisingere at rostlab.informatik.tu-muenchen.de wrote:
> >> >> Hi everybody,
> >> >>
> >> >> I want to add a phosphate to my protein. Is this possible with
> >> gromacs?
> >> >>
> >> >> Thank you
> >> >>
> >> >> --
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> >> > --
> >> > ==================================================================
> >> > Peter C. Lai			| University of Alabama-Birmingham
> >> > Programmer/Analyst		| KAUL 752A
> >> > Genetics, Div. of Research	| 705 South 20th Street
> >> > pcl at uab.edu			| Birmingham AL 35294-4461
> >> > (205) 690-0808			|
> >> > ==================================================================
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> > ==================================================================
> > Peter C. Lai			| University of Alabama-Birmingham
> > Programmer/Analyst		| KAUL 752A
> > Genetics, Div. of Research	| 705 South 20th Street
> > pcl at uab.edu			| Birmingham AL 35294-4461
> > (205) 690-0808			|
> > ==================================================================
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> 
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-- 
==================================================================
Peter C. Lai			| University of Alabama-Birmingham
Programmer/Analyst		| KAUL 752A
Genetics, Div. of Research	| 705 South 20th Street
pcl at uab.edu			| Birmingham AL 35294-4461
(205) 690-0808			|
==================================================================