Simulating the Post Translational modifications in CHARMM forcefield

User discussions
1

GROMACS version: 2022.5
GROMACS modification: NO
Hi everyone,

I have a small question. I am looking to simulate a protein at physiological pH that has multiple phosphorylations 2 Serine (SEP) and 1 Tyrosine (TPO). I know that CHARMM36 support phosphoserine (SP1, SP2 ) and phosphothreonine (TP1, TP2) residues. However, I am confused which one of the two (SP1 or SP2) in the case of serine and which one of the two (TP1 or TP2) in the case of threonine should I select to simulate the protein. Could someone please help me with this.

Many thanks in advance.

Best regards

2

Based on pKa, the dominant form of both at pH 7 will be the SP2 and TP2 forms.

3

Many thanks for answering my query.

Best regards