Well, you will have to make this into a chemically sensible structure. Quite obviously you have hydrogens missing (I assume here the structure is otherwise complete).
________________________________________
From: Arunima Shilpi [writetoash28.gmail.com]
Sent: 01 March 2014 11:11
To: amber.ambermd.org
Subject: [AMBER] error in running antechamber
Dear Sir
Thank you for your reply. I am runnind antechamber for new ligand ZINC3781
having the following co-ordinates.
HETATM 1 C1 DRG 1 30.428 -20.052 29.942 1.00 0.00
C
HETATM 2 C2 DRG 1 30.269 -19.563 31.382 1.00 0.00
C
HETATM 3 O1 DRG 1 31.072 -18.742 31.827 1.00 0.00
O
HETATM 4 C3 DRG 1 29.136 -20.061 32.296 1.00 0.00
C
HETATM 5 C4 DRG 1 28.279 -21.277 31.862 1.00 0.00
C
HETATM 6 C5 DRG 1 26.820 -20.966 31.539 1.00 0.00
C
HETATM 7 C6 DRG 1 26.439 -19.748 30.937 1.00 0.00
C
HETATM 8 C7 DRG 1 25.091 -19.501 30.606 1.00 0.00
C
HETATM 9 C8 DRG 1 24.105 -20.489 30.831 1.00 0.00
C
HETATM 10 C9 DRG 1 24.480 -21.692 31.463 1.00 0.00
C
HETATM 11 C10 DRG 1 25.823 -21.925 31.824 1.00 0.00
C
HETATM 12 O2 DRG 1 22.775 -20.282 30.546 1.00 0.00
O
HETATM 13 C11 DRG 1 22.373 -20.293 29.201 1.00 0.00
C
HETATM 14 C12 DRG 1 22.504 -18.873 28.610 1.00 0.00
C
HETATM 15 C13 DRG 1 21.976 -18.867 27.161 1.00 0.00
C
HETATM 16 C14 DRG 1 20.536 -19.380 27.079 1.00 0.00
C
HETATM 17 C15 DRG 1 20.470 -20.746 27.788 1.00 0.00
C
HETATM 18 O3 DRG 1 21.029 -20.683 29.105 1.00 0.00
O
HETATM 19 C16 DRG 1 19.041 -21.313 27.877 1.00 0.00
C
HETATM 20 O4 DRG 1 18.213 -20.494 28.696 1.00 0.00
O
HETATM 21 C17 DRG 1 17.921 -20.870 29.958 1.00 0.00
C
HETATM 22 O5 DRG 1 18.275 -21.943 30.448 1.00 0.00
O
HETATM 23 C18 DRG 1 17.138 -19.856 30.716 1.00 0.00
C
HETATM 24 C19 DRG 1 16.729 -18.623 30.153 1.00 0.00
C
HETATM 25 C20 DRG 1 16.026 -17.685 30.938 1.00 0.00
C
HETATM 26 C21 DRG 1 15.728 -17.967 32.287 1.00 0.00
C
HETATM 27 C22 DRG 1 16.121 -19.198 32.853 1.00 0.00
C
HETATM 28 C23 DRG 1 16.810 -20.134 32.059 1.00 0.00
C
HETATM 29 O6 DRG 1 15.872 -19.513 34.161 1.00 0.00
O
HETATM 30 O7 DRG 1 15.072 -17.026 33.023 1.00 0.00
O
HETATM 31 O8 DRG 1 15.632 -16.491 30.403 1.00 0.00
O
HETATM 32 O9 DRG 1 20.212 -19.556 25.710 1.00 0.00
O
HETATM 33 O10 DRG 1 22.073 -17.558 26.634 1.00 0.00
O
HETATM 34 O11 DRG 1 21.823 -17.944 29.431 1.00 0.00
O
CONECT 1 2
CONECT 11 10 6
CONECT 13 12 14 18
CONECT 14 15 13 34
CONECT 15 14 33 16
CONECT 16 15 32 17
CONECT 17 16 18 19
CONECT 19 17 20
CONECT 21 20 22 23
CONECT 23 21 24 28
CONECT 24 23 25
CONECT 2 1 4 3
CONECT 25 31 24 26
CONECT 26 25 27 30
CONECT 27 26 28 29
CONECT 28 23 27
CONECT 4 2 5
CONECT 5 6 4
CONECT 6 11 7 5
CONECT 7 6 8
CONECT 8 9 7
CONECT 9 12 10 8
CONECT 10 11 9
CONECT 3 2
CONECT 33 15
CONECT 34 14
CONECT 12 9 13
CONECT 18 13 17
CONECT 20 19 21
CONECT 22 21
CONECT 29 27
CONECT 30 26
CONECT 31 25
CONECT 32 16
END
When I run the command for antechamber
antechamber -i ZINC3781.pdb -fi pdb -o ZINC3781.mol2 -fo mol2 -c bcc
it gives the following error
QMMM: ERROR!
QMMM: Unable to achieve self consistency to the tolerances specified
QMMM: No convergence in SCF after 1000 steps.
QMMM: E = -0.1073E+07 DeltaE = -0.3454E+01 DeltaP = 0.4578E-01
QMMM: Smallest DeltaE = -0.4708E-01 DeltaP = 0.4521E-01 Step = 33
kindly guide me in debugging the error.
Regards
Arunima
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Received on Sat Mar 01 2014 - 07:00:02 PST
