Dear Mubasher,

Today only, I also got the same issue.

I resolved the issue by renaming the atoms (C, N or O).

Just check the ATP, there may be same atom number assigned for different atom types.

Like:- for all carbons it is mentioned only C. You should rename them C1, C2, C3 and so on.

Same you have to do for other atoms like N and O present in your ATP.

Like if this is your cordinates:-

HETATM 1 C UNK B 200 20.899 41.890 25.004 1.00 0.00 D C

HETATM 2 C UNK B 200 21.603 40.638 22.570 1.00 0.00 D C

HETATM 3 C UNK B 200 20.554 40.121 23.352 1.00 0.00 D C

HETATM 4 C UNK B 200 20.201 40.745 24.560 1.00 0.00 D C

HETATM 5 C UNK B 200 21.956 42.400 24.215 1.00 0.00 D C

HETATM 6 C UNK B 200 22.310 41.780 23.002 1.00 0.00 D C

HETATM 7 C UNK B 200 20.542 42.518 26.218 1.00 0.00 D C

HETATM 8 C UNK B 200 20.189 41.745 27.343 1.00 0.00 D C

HETATM 9 C UNK B 200 19.832 42.368 28.549 1.00 0.00 D C

HETATM 10 C UNK B 200 19.826 43.773 28.652 1.00 0.00 D C

HETATM 11 C UNK B 200 20.182 44.560 27.530 1.00 0.00 D C

HETATM 12 C UNK B 200 20.535 43.927 26.322 1.00 0.00 D C

HETATM 13 O UNK B 200 21.912 40.019 21.406 1.00 0.00 D O

HETATM 14 CL UNK B 200 23.580 42.428 22.084 1.00 0.00 D C

HETATM 15 CL UNK B 200 19.387 44.460 30.139 1.00 0.00 D C

HETATM 16 CL UNK B 200 20.205 46.255 27.574 1.00 0.00 D C

HETATM 17 H UNK B 200 21.282 40.042 20.696 1.00

Here C, CL and O has same residue number i.e. 200.

So, you can modify them in this way:-

HETATM 1 C1 UNK B 200 20.899 41.890 25.004 1.00 0.00 D C

HETATM 2 C2 UNK B 200 21.603 40.638 22.570 1.00 0.00 D C

HETATM 3 C3 UNK B 200 20.554 40.121 23.352 1.00 0.00 D C

HETATM 4 C4 UNK B 200 20.201 40.745 24.560 1.00 0.00 D C

HETATM 5 C5 UNK B 200 21.956 42.400 24.215 1.00 0.00 D C

HETATM 6 C6 UNK B 200 22.310 41.780 23.002 1.00 0.00 D C

HETATM 7 C7 UNK B 200 20.542 42.518 26.218 1.00 0.00 D C

HETATM 8 C8 UNK B 200 20.189 41.745 27.343 1.00 0.00 D C

HETATM 9 C9 UNK B 200 19.832 42.368 28.549 1.00 0.00 D C

HETATM 10 C10 UNK B 200 19.826 43.773 28.652 1.00 0.00 D C

HETATM 11 C11 UNK B 200 20.182 44.560 27.530 1.00 0.00 D C

HETATM 12 C12 UNK B 200 20.535 43.927 26.322 1.00 0.00 D C

HETATM 13 O13 UNK B 200 21.912 40.019 21.406 1.00 0.00 D O

HETATM 14 CL1 UNK B 200 23.580 42.428 22.084 1.00 0.00 D C

HETATM 15 CL2 UNK B 200 19.387 44.460 30.139 1.00 0.00 D C

HETATM 16 CL3 UNK B 200 20.205 46.255 27.574 1.00 0.00 D C

HETATM 17 H1 UNK B 200 21.282 40.042 20.696 1.00

This strategy worked for me.

Hope, it may work for you too.

Better you can use Patch Dock online server for Protein-Protein Docking

Dear Vikram,

ATP atoms were already assigned unique atom numbers/names. HADDOCK was showing such errors from last four days, but it has now started working with the same files without any errors.

Thanks for your time.

Dear Selva,

Thank you for suggesting Patch Dock. I ll definitely look into it.

Dear Mubasher,

Good to hear that docking is started.

Cheers.