Hello Xiaoquan,
Using the coordinates posted in your original email, one can see that the H14 atom has the same x,y,z coordinate values as the O1 atom. When you display it in VMD the two atoms will overlap, with the oxygen radius being bigger in a ball-and-stick representation. There could be a few reasons why this occurs, including poor input structure and the force-field parameters.
You can check how well the GAFF force-field parameters, as given by antechamber's frcmod output file, reproduce quantum potential energies curves by using the Wolf2Pack (W2P) website. An analogue molecule that encompasses your R-beneze-SO3H residue is benzenesulfonic acid. W2P has the two torsion rotational curves available for checking: C-S-O-H and C-C-S-O. Once you verify that the atom types are the same as you have defined in your molecule (see step 5 of W2P's workflow), can copy and paste the frcmod file into the force-field text box at the last step of the workflow.
If you have any questions or problems concerning W2P, please use its message board for communication. There are a few tutorials on the website that will introduce you to force fields and their optimization if you are new to the ideas.
Best regards,
Karl
----- Original Message -----
From: "Xiaoquan Sun" <xs005.email.uark.edu>
To: "amber" <amber.ambermd.org>, "amber-subscribe" <amber-subscribe.ambermd.org>
Sent: Thursday, July 4, 2013 6:28:38 AM
Subject: [AMBER] Abnormal simulation in the sulfonic acid group.
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.
--------------
Xiaoquan Sun
2013-07-03
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Received on Thu Jul 04 2013 - 03:00:02 PDT
