Dear official,
I am doing MD simulation with GAFF, but the sulfonic acid group became a three-membered ring which includes two oxygen atom and one sulphur atom. Before the simulation, the sulfonic acid group is normal. But after a few times' simulation, I can not find the hydrogen that linked with one oxygen atom of the sulfonic acid group in VMD, although I can find the item in PDB files. The pdb file is following, I just want to find out H14 which belonged to the sulfonic acid gourp.
ATOM 1 C1 SSH X 1 7.831 -4.157 -1.597 0.00 0.00
ATOM 2 H1 SSH X 1 8.043 -4.618 -2.530 0.00 0.00
ATOM 3 C2 SSH X 1 8.482 -4.514 -0.375 0.00 0.00
ATOM 4 S1 SSH X 1 9.821 -5.698 -0.487 0.00 0.00
ATOM 5 O1 SSH X 1 10.658 -5.080 0.628 0.00 0.00
ATOM 6 O2 SSH X 1 10.415 -6.015 0.916 0.00 0.00
ATOM 7 H14 SSH X 1 10.680 -5.077 0.641 0.00 0.00
ATOM 8 O3 SSH X 1 10.667 -5.404 -1.607 0.00 0.00
ATOM 9 C3 SSH X 1 8.060 -3.964 0.870 0.00 0.00
ATOM 10 H2 SSH X 1 8.470 -4.340 1.784 0.00 0.00
ATOM 11 C4 SSH X 1 7.235 -2.848 0.800 0.00 0.00
ATOM 12 H3 SSH X 1 6.919 -2.351 1.720 0.00 0.00
ATOM 13 C7 SSH X 1 6.989 -3.031 -1.534 0.00 0.00
ATOM 14 H5 SSH X 1 6.419 -2.634 -2.453 0.00 0.00
ATOM 15 C5 SSH X 1 6.728 -2.325 -0.345 0.00 0.00
ATOM 16 C6 SSH X 1 5.872 -1.071 -0.332 0.00 0.00
ATOM 17 H4 SSH X 1 6.018 -0.748 0.702 0.00 0.00
ATOM 18 C8 SSH X 1 4.430 -1.415 -0.660 0.00 0.00
ATOM 19 H6 SSH X 1 3.681 -0.645 -0.478 0.00 0.00
ATOM 20 H7 SSH X 1 4.114 -2.330 -0.216 0.00 0.00
Sincerely,
Xiaoquan Sun.
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Xiaoquan Sun
2013-07-03
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Received on Wed Jul 03 2013 - 21:00:03 PDT
