[gmx-users] Serine phosphorylation

[Catarina A. Carvalheda dos Santos]

Hi Simone,

You can simply build the serine phosphoryl group (PO3) using PyMOL or any
other graphics system that allows you to do this. In case of PyMOL you can
easily find instructions online. Avoid clashes with other atoms or you'll
have problems while minimising the system.

Change the name of the phosphorylated serine to S2P (phosphoserine in
amber) using a text editor.

Then run the pdb2gmx and, if you did everything correctly, you should now
have a topology of your phosphorylated  system.

The rest of the steps should not be a mystery for you. Add water and ions,
minimise and equilibrate the system, and finally run the MD simulations. In
any case, there are several tutorials available in the GROMACS website
concerning these steps.

Hope this helps.

Cheers
On 10 Jan 2016 09:09, "Simone Bolognini" <simo.bolognini at gmail.com> wrote:

> Thank you for your support, but I find the instructions on the website
> extremely unclear to me. There are some commands to be run which are nor
> gromacs neither bash commands that pretty puzzle me. However, I'd better be
> more specific in explaining my problem: I have a protein whose pdb contains
> a particular serine in which I am interested on. Now, for some reasons, I
> need to change this serine (and only this one!) to a phosphorylated one and
> run some MD production using AMBER-ILDN with this new configuration. What
> should I do exactly? Can you provide me a sequence of steps which I should
> follow in order to go from the starting pdb to the actual simulation?
>
> As always, thank you very much for your help!
> Simone
>
> Il giorno ven 8 gen 2016 alle ore 13:30 Changrong Ge <
> changrong.ge at gmail.com>
> ha scritto:
>
> > http://selene.princeton.edu/FFPTM/
> >
> > On Fri, Jan 8, 2016 at 9:52 AM, Simone Bolognini <
> simo.bolognini at gmail.com
> > >
> > wrote:
> >
> > > Hi everyone,
> > > I need to run some MD simulations with a protein where a particular
> > serine
> > > should be phosphorylated. Since in the original pdb the serine is
> > actually
> > > not, I guess I should modify something 'by hand'. I'm going to use
> > > AMBER-ILDN ff. Can anyone of you tell me what should I do? My first
> guess
> > > was to generate the topology and then directly substitute my serine
> with
> > > the phosphorylated one (looking for the AMBER-ILDN parameters), but
> > > sincerely I don't know if this is the correct way to proceed.
> > >
> > > Thanks a lot for your support!
> > > Simone
> > > --
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> >
> >
> > --
> >
> > Changrong Ge, PhD
> >
> > Division of Medical Inflammation Research
> > Department of Medical Biochemistry and Biophysics (MBB)
> > Karolinska Institutet
> > Scheeles väg 2, B2 Plan 4
> > SE-171 77 Stockholm
> > Sweden
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> or
> > changrong.ge at gmail.com
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