![]() ![]() In order to configure HADDOCK, call the install.csh script with as argument the configuration script you just created: Set CNSTMP=/home/software/cns/cns_solve-1.31-UU-Linu圆4bits.exeįor submitting to a batch system instead you might want to use a wrapper script. QUEUESUB defining the HADDOCK python script used to run the jobs (the default QueueSubmit_concat.py should do in most cases).Īnd example configuration file for running on local resources assuming a 4 core system would be: NUMJOB defining the number of concurrent jobs executed (or submitted). ![]() either via csh or through a specific command submitting to your local batch system) QUEUETMP defining the submission command for running the jobs (e.g. This configuration file should contain the following information:ĬNSTMP defining the location of your CNS executable Then activate the haddock2.4 environment with:Įdit then a configuration file specific to your system. In case you installed miniconda, create a HADDOCK2.4 environment with theįollowing command (withing the haddock2.4 directory): It is used throughout our tutorials.Īfter having downloaded HADDOCK, unpack the archive under the installation directory with the following command: For information and download see the ProFit webpage. The latter should notify the authors that they are using it. Profit can be obtained free of charge for both non-profit and commercial users. Some of the provided analysis tools in HADDOCK make use of Profit. ProFit is designed to be the ultimate protein least squares fitting program. In case git is not installed on your system, go the GitHub site given in the command and download directly the archive. PDB-tools is a useful collection of Python scripts for the manipulation (renumbering, changing chain and segIDs…) of PDB files is freely available from our GitHub repository. Rename it to reduce if needed and make sure it is executable (e.g. Put the executable for example in ~software/bin or some other software installation directory in your path, You can directly download the reduce executable for Linux or OSX. An pre-compiled executable can be freely downloaded from the MolProbity GitHub website. In the context of HADDOCK we are making use of MolProbity to define the protonation state of Histidine residues using the reduce application. MolProbity is a structure validation software suite developed in the Richardson lab at Duke University. HADDOCK-tools** is collection of HADDOCK-related scripts freely available from our GitHub repository. configure \-\-disable-json \-\-disable-xml \-\-prefix ~/software Here we will assume you save the tar archive under the software directory in your home directory: If running into problems you might want to disable json and xml support. Following the download and installation instructions from the FreeSASA website. In order to identify surface-accessible residues to define restraints for HADDOCK we can make use of NACCESS freely available to non-profit users, or its open-source software alternative FreeSASA. DSSP (only required to use the coarse-graining option in HADDOCK2.4)ĭSSP is required to define the secondary structure, an information required to select the proper backbone parameter for the Martini coarse grained model (see coarse graining PDB files for docking. Biopython 1.72 (only required to use the coarse-graining option in HADDOCK2.4)īiopython version 1.72 is required in order to be able to convert the atomistic models into coarse grained models (see coarse graining PDB files for docking. Importantly, python2 (pointing to python2.7) should be existing on your system.Īs python2.7 is end of life, one way to install it is to use miniconda on your system. Python version 2.7 is required in order to run HADDOCK2.4. Consult also for some guidance the related entry in the HADDOCK forum Python2.7 In order to get access to all features of HADDOCK you will need to recompile CNS using the additional files provided in the HADDOCK distribution in the cns1.3 directory. CNS is freely available for non-profit organisations. The other required piece of software to run HADDOCK is its computational engine, CNS (Crystallography and NMR System – ). To obtain HADDOCK2.4 fill the HADDOCK license form ). DSSP (only required to use the coarse-graining option in HADDOCK2.4). ![]() Biopython 1.72 (only required to use the coarse-graining option in HADDOCK2.4). ![]()
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