Does anyone know why am I getting an error message using HADDOCK web server?


#1

It shows “Your HADDOCK run has encountered errors and was aborted”

Status: FAILED
There was an error in the simulated annealing stage of the docking.
How could I solve this problem?

Thank you in advance


#2

Many possible reasons why it1 could fail.
Search for error messages in the output of it1 (there should be one provided on the webpage of your run - look for ERR in the file).


#3

Hi, this is kind of message that appears in error file:

%PARRDR-ERROR: duplication of bond HC NC2
%PARRDR-ERROR: duplication of angle CH2P CH2E HA
PARRDR> end
%PARRDR-ERROR: duplication of bond HC NC2
%PARRDR-ERROR: duplication of bond OUF SUF
%PARRDR-ERROR: duplication of angle CH2P CH2E HA
%PARRDR-ERROR: duplication of angle OUF SUF OUF
%PARRDR-ERROR: duplication of nonbonded entry SUF
%PARRDR-ERROR: duplication of nonbonded entry OUF

XRDECODE-ERR: Illegal argument(s).:
evaluate ($resid2=encode(decode($resid1)+1))
^
%EVALUATE-ERR: EVALUATE assignment aborted.:
evaluate ($resid2=encode(decode($resid1)+1))
^
SHOW: sum over selected elements = 1.000000
( B VAL 111 N ) 2219.0


#4

Are you running a local version of HADDOCK? Did you manually define the flexible regions?
If this is the case, there must be a typo in your run.cns


#5

I am using the easy interface to the HADDOCK web server and I did not define the flexible regions.


#6

Without more information on your system (what kind of molecules are you docking) we can’t do much… Also are you using the 2.2 version of the server?


#7

I had problems with dimers first pdb ( contains multiple forms of the same residue), and second pdb 2 (Unable to generate topology for ligand MOH. PRODRG did not create the required output; pdb file contains multiple residues with number 5 in chain A), and I fixed this using PDB tools. I am using 2.2 version.


#8

Send me via email your PDB - there is something fishy in your system
Did you read all the related other threads in ask.bioexcel.eu?


#10

Do you really believe that, even doing our best, we can help you when zero information is provided …???