# Protein-small molecule docking
**URL:** https://ask.bioexcel.eu/t/protein-small-molecule-docking/262
**Category:** HADDOCK
**Created:** [December 26, 2016, 7:21am UTC](https://ask.bioexcel.eu/t/protein-small-molecule-docking/262 "2016-12-26T07:21:59Z")
**Posts on this page:** 4
**Page:** 1
### Author:  [@William\_Chong](https://ask.bioexcel.eu/u/William_Chong)
#### Post date: [December 26, 2016, 7:21am UTC](https://ask.bioexcel.eu/t/protein-small-molecule-docking/262/1 "2016-12-26T07:21:59Z")
The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to [http://www.bonvinlab.org/software/haddock2.2](http://www.bonvinlab.org/software/haddock2.2)
I am encountering an error when I am submitting a protein-ligand system on the web-server, using the easy interface service.
The error read as: Second pdb file contains multiple residues with number 0 in chain A
It is a ligand and it should contain only ONE residue.
How should I make the system to read the ligand correctly?
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [December 26, 2016, 12:58pm UTC](https://ask.bioexcel.eu/t/protein-small-molecule-docking/262/2 "2016-12-26T12:58:35Z")
The ligand should have only one residue, and all atom names should be unique.
Check your ligand PDB for this.
---
### Author:  [@diffracteD](https://ask.bioexcel.eu/u/diffracteD)
#### Post date: [April 4, 2017, 6:58pm UTC](https://ask.bioexcel.eu/t/protein-small-molecule-docking/262/3 "2017-04-04T18:58:18Z")
That helped to pass the initial formatting check but raised a different error:
RUN\_NUMBER 1
HADDOCK\_DIR /home/enmr/software/haddock2.2-grid
submit\_save Save updated parameters
PROT\_SEGID\_2 B
PROT\_SEGID\_1 A
PDB\_FILE1 protein1.pdb
AMBIG\_TBL ambig.tbl
PROJECT\_DIR /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000061
PDB\_FILE2 protein2.pdb
looking for existing files
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000061/run1/begin/protein2.psf…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000061/run1/begin/protein2.pdb…
waterdock false
waiting for the psf files…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000061/run1/begin/protein2.psf…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000061/run1/begin/protein2.pdb…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000061/run1/begin/protein2.psf…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000061/run1/begin/protein2.pdb…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000061/run1/begin/protein2.psf…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000061/run1/begin/protein2.pdb…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000061/run1/begin/protein2.psf…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000061/run1/begin/protein2.pdb…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000061/run1/begin/protein2.psf…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000061/run1/begin/protein2.pdb…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000061/run1/begin/protein2.psf…
waiting for /home/enmr/services-enmr/HADDOCK2.2/server/run/userrun000061/run1/begin/protein2.pdb…
Error in the topology generation: prot\_psf\_B could not be created
=\> HADDOCK stopped
##############################################################################
Finishing HADDOCK on: 2017-04-04 21:15:36
Au revoir.
Tot ziens.
Bye bye.
Cleaning up HADDOCK run directory
Only files for structure #1 will be kept…
---
### Author:  [@amjjbonvin](https://ask.bioexcel.eu/u/amjjbonvin)
#### Post date: [April 5, 2017, 8:12am UTC](https://ask.bioexcel.eu/t/protein-small-molecule-docking/262/4 "2017-04-05T08:12:36Z")
Still an issues with your ligand naming…