[gmx-users] Is TRO defined correctly in the ffG43a1p forcefield file?

Kirill Bessonov kbessonov at gmail.com
Sun Mar 4 22:44:14 CET 2012

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

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

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?

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