[gmx-users] Serine phosphorylation

[Simone Bolognini]

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