this is the command,
pdb2gmx -f dioxin.pdb -o di.pdb -p di.top -ter
Here I have attached the dioxin.pdb file.
IN di.pbd there is no CL atoms.
NIlesh
REMARK Accelrys Discovery Studio PDB file
REMARK Created: Sat Nov 14 17:45:28 Eastern Standard Time 2009
ATOM 1 O1 PCD 1 0.000 -1.428 0.001 1.00 0.00 O
ATOM 2 C2 PCD 1 1.172 -0.699 0.001 1.00 0.00 C
ATOM 3 C3 PCD 1 1.172 0.700 0.001 1.00 0.00 C
ATOM 4 O4 PCD 1 0.000 1.428 0.001 1.00 0.00 O
ATOM 5 C5 PCD 1 -1.172 0.700 0.001 1.00 0.00 C
ATOM 6 C6 PCD 1 -1.172 -0.700 0.001 1.00 0.00 C
ATOM 7 C7 PCD 1 2.372 1.395 0.000 1.00 0.00 C
ATOM 8 C8 PCD 1 3.586 0.700 -0.000 1.00 0.00 C
ATOM 9 C9 PCD 1 3.586 -0.700 -0.000 1.00 0.00 C
ATOM 10 C10 PCD 1 2.372 -1.395 0.000 1.00 0.00 C
ATOM 11 C11 PCD 1 -2.372 1.395 0.000 1.00 0.00 C
ATOM 12 C12 PCD 1 -3.586 0.700 -0.000 1.00 0.00 C
ATOM 13 C13 PCD 1 -3.586 -0.700 -0.000 1.00 0.00 C
ATOM 14 C14 PCD 1 -2.372 -1.395 0.000 1.00 0.00 C
ATOM 15 CL1 PCD 1 5.070 1.618 -0.001 1.00 0.00 CL
ATOM 16 CL2 PCD 1 5.070 -1.618 -0.001 1.00 0.00 CL
ATOM 17 CL3 PCD 1 -5.070 1.618 -0.001 1.00 0.00 CL
ATOM 18 CL4 PCD 1 -5.070 -1.618 -0.001 1.00 0.00 CL
ATOM 19 H19 PCD 1 2.359 -2.478 0.000 1.00 0.00 H
ATOM 20 H20 PCD 1 2.359 2.478 0.000 1.00 0.00 H
ATOM 21 H21 PCD 1 -2.359 -2.478 0.000 1.00 0.00 H
ATOM 22 H22 PCD 1 -2.359 2.478 0.000 1.00 0.00 H
END
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