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).
Thanks.
Sincerely,
Keretsu
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Received on Tue Aug 20 2019 - 02:30:02 PDT
