Which patch to use for modeling phospho threonine THP1 or THPB

User discussions
1

GROMACS version:2022.5
GROMACS modification: No

Hi,

I am trying to simulate a protein in water. I am confused which patch to use out of THP1 or THPB for modeling phospho threonine. Th pH at which I am trying to run the simulations is neutral (7.2). I understand what selections I have to make for serines and tyrosines since based on pKa, the dominant form of both at pH 7 will be the SP2 and TP2 forms. Could some one answer that for me?

thanks in advance

Best regards

2

Hi,

I would be grateful if someone can help me in figuring this out.

Many thanks and regards

3

Hi,

I am new to this field and would be really grateful if someone can answer this query.

@hess

Thanks in advance and sorry for asking repeatedly.

4

I don’t really know what you are talking about. I assume that “patch” refers to a method of modifying a residue in a force field. If that is correct, then that is a question for the force field, not for GROMACS.