Dear all, I am trying to run simulation with phosphorylated Threonine (TRO) and I found lot's of info about this issue reading previous posts which explained on how to patch the force-field files and define this modified amino acid. After looking at the community forcefield offered here http://www.gromacs.org/Downloads/User_contributions/Force_fields
After exploring those files what calls my attention is that in the *.hdb file that describes which atoms are protonated is seems to have an issue that I wanted to double-check with the rest of the members. It seems to me that the CH3 group is not protonated in the phosphotyrosine (TRO) as shown below Extracted from *.hdp file THR 2 1 1 H N -C CA 1 2 HG1 OG1 CB CA TPO 1 1 1 H N -C CA ...but where is the 2nd line??? Why THR has 2 lines why the TRO having the PO3 group has only one line? Can somebody explain this? Kirill
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