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

Najamuddin Memon najamuddinmemon63 at gmail.com
Mon Feb 11 18:42:26 CET 2019

Dear use 43a1 extended phosphorylated force field. Although phosphorylated
amino acids are not in the active site or not involved in the interaction
with ligand but in broad context these phosphorylated residues have impact
on structure of protein over the function of time

On Mon, Feb 11, 2019, 6:32 PM Swapnil Bhujbal <swapnilbhujbal18 at gmail.com

> 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.
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