How to run FITTED on more than one processor?

Solution:

 We encourage the use of script to distribute different instances of FITTED over the number of processors you want to use. You can find a general script below. However, if you plan to run FITTED on a cluster computer, we highly suggest you to use the corresponding tools (bqtool, PBS, etc.) installed on your cluster.

We will illustrate the use of scripts for two different examples:

1. In the first example, we will consider the use of 4 processors on the same computer. We will also consider only 1 protein system, having a list of 100 ligands to dock. Then, the strategy involves the creation of four scripts, one for each processor.

 Since there is only one protein used, the strategy is to split the list of ligands in 4 different files. Please refer to the FAQ "How to screen many ligands " in order to get the scripts and the procedure. You then need to create four scripts that point to the corresponding ligand lists.

2. The second example will highlight the use of 4 processors with 16 different protein systems, each having a list of 100 ligands to dock.

Now we need a more complex script that will create the keyword files on-the-fly for the corresponding ligands of the list.txt and execute the FITTED run automatically similar to the example above. However, since we have more than one protein system, we need to also create a list of the protein to be used. The script is available in the Download section .

You need a file named list.txt that contains the filenames of the ligands (one per line such as ligand1.mol2, ligand2.mol2, etc...) and four list_pro[1-4].txt files that contain each 4 different protein systems. Thus, four differents scripts will launch FITTED on the set of 4 different protein systems for each the list of the 100 ligands to dock.

 The files needed to be modified are the following:

list.txt

- You need to create the list of your ligands (with the .mol2 extension)

list_pro1.txt, list_pro2.txt, list_pro3.txt, list_pro4.txt

- Each file contains four different protein systems that yiou want to run. Technically, the file lists the name of the folders to navigate to and execute FITTED.

template.txt

 - this is the general keyword file which contains all the docking settings. You need to modify with the proper Protein name, BindSite and IS files.

script1.sh, script2.sh, script3.sh, script4.sh and run.sh

 -  these are the scripts to execute. The command to use is the following:

 prompt$ sh run.sh &

 - Note that you need to have the following folder structure. All the files mentioned above need to be place and executed from the Working Dir folder.