Is there any difference between "SEP" as a non standard residue and phohophorylated serine?

01 February 2021 1 6K Report

I am trying to run a molecular dynamics simulation for a ligand that contains a "SEP" residue. also, I am preparing my files using Charmm-GUI using charmm36 ff, but it says that it will rename my "SEP" into SER and will phosphorylate it as a workaround.

My question is will my ligand be the same if this happened? or I need to create parameters and topology files?

hope I will find an answer!

Abdo A Elfiky

You can try it and check what you will get in the generated files.

SEP is the phosphorylated serine and couldn't be readable in all FF.

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