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
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?
The ligand should have only one residue, and all atom names should be unique.
Check your ligand PDB for this.
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
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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…
Still an issues with your ligand naming…