[gmx-users] Phosphorylated serine and threonine residues (Gromacs MD)

[Swapnil Bhujbal]

Dear all,

I am working with a protein having phosphorylated serine and threonine
residues. I will be performing ligand-protein MD. These phosphorylated
amino acid residues are not located in the active site of protein.
Should I just replace the phosphorylated serine and threonine residues with
serine and threonine before MD preparations? Or shoild I ignore them
because they will not be involved in any interactions with the ligand? Or
do we have different force fields for the phosphorylated residues ?

Your suggestions are highly appreciated.

Thank you.

Sincerely,
Mr. Swapnil Bhujbal
PhD Scholar,
School of Medicine,
Chosun University,
South Korea.