AW: [gmx-users] Adding phosphate to protein

[Rausch, Felix]

There is a G43a1 modification available with phosphorylated amino acids in the users contribution section of the Gromacs homepage. http://www.gromacs.org/Downloads/User_contributions/Force_fields

It was uploaded by Graham Smith and Justin made it compatible with the Gromacs 4.5.x versions, so maybe this would be a good starting point for your modified residue.

Good luck.

-----Ursprüngliche Nachricht-----
Von: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] Im Auftrag von reisingere at rostlab.informatik.tu-muenchen.de
Gesendet: Montag, 3. September 2012 10:07
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] Adding phosphate to protein

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
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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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