HADDOCK is for protein-protein or protein-nucleic acid docking. It cannot dock small molecules, such as your acid.

You should look into protein-ligand docking, with software such as AutoDock.

You can find answer to your problem here...

http://www.nature.com/nprot/journal/v5/n5/box/nprot.2010.32_BX3.html

Nonoverlapping numbering: During the docking process, every molecule is reduced to a single chain. Therefore, in case of a multichain molecule, one can select a chain to be used or select all the chains. However, in the latter case, there must be no overlap in numbering between the chains. For example, a molecule with chain A residue 1–100 and chain B residue 101–200 is acceptable; a molecule with residue 1–100 for both chains A and B is not. If this is the case, one must renumber the PDB structure.....

from the article

Nature Protocols 5, - 883 - 897 (2010)

Published online: 15 April 2010 | doi:10.1038/nprot.2010.32

Subject Category: Computational and theoretical biology

The HADDOCK web server for data-driven biomolecular docking

Sjoerd J de Vries1, Marc van Dijk1 & Alexandre M J J Bonvin1

So in your case for the B segment change the numbering of the residues to 104

Hi Karthick Thangavel

Firstly concerning HADDOCK, as Fotis Baltoumas pointed out, it is meant for docking larger biomolecules

And secondly addressing your issue with numbering, when you remove any residue, or change the actual sequence in a pdb file, there are the chances for the formation of overlapping numbers. This can be rectified using online renumbering servers, where all the constituents of your multiple chains get sequentially numbered, thereby prevents number overlapping.

The below link will take you to an online renumbering tool:

https://swift.cmbi.umcn.nl/servers/html/renumb.html

Hope it helps.

I am also getting a similar error message. My input PDBs contain no multiple occupancy atom and more interestingly the reported atomic coordinate (x,y,z) is not to be found in them. Here, the receptor contains 3 chains with identical residue numbers and types while they are distinct in their chain IDs (A, B, C). I am not getting the requirement for renumbering in my case. All residues are unique if viewed together with their chain IDs. Any advice would be deeply appriciated.

Error message: First pdb file contains multiple forms of the same residue. This is not supported in the current form. If you would like to supply multiple conformations, please create an ensemble ATOM    295  N  AHIS A 145      20.942 -24.071 -10.119  0.50 22.04           N

I am also getting a similar error message. My input PDBs contain no multiple occupancy atom and more interestingly the reported atomic coordinate (x,y,z) is not to be found in them. Here, the receptor contains 3 chains with identical residue numbers and types while they are distinct in their chain IDs (A, B, C). I am not getting the requirement for renumbering in my case. All residues are unique if viewed together with their chain IDs. Any advice would be deeply appriciated.

Error message: First pdb file contains multiple forms of the same residue. This is not supported in the current form. If you would like to supply multiple conformations, please create an ensemble ATOM    295  N  AHIS A 145      20.942 -24.071 -10.119  0.50 22.04           N

This renumbering tool works fine or you need to refine t5he structure in maestro-desmond it is free. https://swift.cmbi.umcn.nl/servers/html/renumb.html