[gmx-users] Topology for phosphorylated protein in gromacs using Amber Forcefield

[Seketoulie Keretsu]

Dear Expert,

I know this issue has been raised earlier  by others but I'm still having
trouble with generating topology files for a phosphorylated protein,
phosphorylated at Tyrosine 1034 residue. I am using gromacs2018 and
Amber99SB protein as FF. The residue in the PDB file is shown below.

ATOM   1294  N   PTR A1034      -2.670 -10.279 -15.822  1.00 16.60           N
ATOM   1295  CA  PTR A1034      -2.446  -9.183 -16.725  1.00 16.94           C
ATOM   1296  C   PTR A1034      -3.533  -8.144 -16.622  1.00 18.89           C
ATOM   1297  O   PTR A1034      -4.612  -8.406 -16.068  1.00 19.06           O
ATOM   1298  CB  PTR A1034      -2.291  -9.698 -18.159  1.00 18.90           C
ATOM   1299  CG  PTR A1034      -3.542 -10.337 -18.686  1.00 24.64           C
ATOM   1300  CD1 PTR A1034      -3.802 -11.695 -18.501  1.00 22.99           C
ATOM   1301  CD2 PTR A1034      -4.492  -9.556 -19.348  1.00 23.91           C
ATOM   1302  CE1 PTR A1034      -4.980 -12.268 -18.990  1.00 23.96           C
ATOM   1303  CE2 PTR A1034      -5.639 -10.107 -19.829  1.00 26.74           C
ATOM   1304  CZ  PTR A1034      -5.884 -11.455 -19.654  1.00 32.04           C
ATOM   1305  OH  PTR A1034      -6.953 -11.808 -20.159  1.00 41.31           O
ATOM   1306  P   PTR A1034      -7.810 -13.106 -19.896  1.00 46.59           P
ATOM   1307  O1P PTR A1034      -9.076 -12.851 -20.613  1.00 45.47           O
ATOM   1308  O2P PTR A1034      -8.107 -13.257 -18.394  1.00 55.84           O1-
ATOM   1309  O3P PTR A1034      -6.994 -14.285 -20.476  1.00 42.59           O

As advised in some previous letters, I copied residuetypes.dat and
added "PTR" to it.
I have also tried
http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field#Adding_a_new_residue

Some experts mentioned modern amber FF can handle phosphorylated
residues. But, I can't seem to find the right way to do it.

query 1: Please advise how to go about this. I have never worked on
Phosphorylated

residues and have no like minded people to discuss with. A brief step
wise instruction would really help me and others

doing this for the first time (this problem has been asked frequently
on Research gate and here too).

query 2: should atom be treated at ATOM or HETATM ?

Thanks.

Sincerely,

Keretsu