Installation error

HADDOCK
1

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

Dear users,

I am getting an error message after running haddock2.2 :

Traceback (most recent call last):
File “/home/ula/Programs/haddock2.2/Haddock/RunHaddock.py”, line 249, in
run = InputFileParser.ParseRunCns() #define a dictionary run (variablename:value)
File “/home/ula/Programs/haddock2.2/Haddock/DataIO/InputFileParser.py”, line 108, in ParseRunCns
variablevalue[head][t] = vvv
TypeError: ‘str’ object does not support item assignment

any suggestions

best reagrds
Urszula

2

Running a local version of HADDOCK I assume?

This looks like a problem in your run.cns
Do check its format, compare with an original file from the HADDOCK distribution

3

I am trying to run a local version of HADDOCK 2.2. I did not change the run.cns. I am running examples from the haddock directory …I do not know what is the problem.

run.cns
! The file containing all parameters for HADDOCK
!
! ***********************************************************************
! * Copyright 2003-2015 Alexandre Bonvin, Utrecht University. *
! * Originally adapted from Aria 1.2 from Nilges and Linge, EMBL. *
! * All rights reserved. *
! * This code is part of the HADDOCK software and governed by its *
! * license. Please see the LICENSE file that should have been included *
! * as part of this package. *
! ***********************************************************************
!
module(
iteration;
filenames;
data;
iterations;
saprotocol;
refine;
toppar;
analysis;
)

{+ File: run.cns +}
{+ Description: this file contains all necessary information to run HADDOCK. +}

{+ Authors: Alexandre Bonvin +}
{+ Version: 2.2, 2013 +}
{+ Initially adapted from ARIA of Nilges and Linge +}

{+ Please cite the following references when using this protocol: +}
{+ reference: Cyril Dominguez, Rolf Boelens and Alexandre M.J.J. Bonvin (2003). HADDOCK: a protein-protein docking approach
based on biochemical and/or biophysical information. J. Am. Chem. Soc. 125, 1731-1737.

4

Which python version are you using? Should be 2.7.X

5

I am using python 2.7.

6

I have installed python 3 as well but I edited haddock scripts and changed i to 2.7.

7

Hi Urszula,

This error has two probable causes:

  1. You accidentally changed something in the InputFileParser.py file.
  2. Your run.cns file has an invalid value somewhere. Unfortunately our parser will not tell you where.

Could you share your full run.cns file with us? You can e-mail it to me at joaor@stanford.edu. In between, make sure your InputFileParser.py file has not been edited somehow.