[gmx-users] Serine phosphorylation

[Changrong Ge]

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
Tel:  +46-8-524 86337 ,   Mobile: +46-(0)76-2878 029
Fax: +46-8-524 87750 ,  Email: changrong.ge at ki.se <changrong at dbb.su.se> or
changrong.ge at gmail.com