Just click on analyze , load the dlg file, then the macromolecule and then click on play molecules ranked by energy. Then the molecule with the lowest energy will be displayed first. Click on write conformation, then build complex, then write complex. This complex file would be saved in pdbqt format. You can change it to pdb format by opening it in pymol.

Sorry Archit but Parmeswaran is asking not to writing the cluster manually every time but it should be an automated process as one cant to the same process for 20,000 times. Am I right

The lowest energy conformation of the ligand in each cluster is written out after 'LOWEST ENERGY DOCKED CONFORMATION from EACH CLUSTER" in the .dlg file.

So, how about writing a python script to 1) parse the "CLUSTERING HISTOGRAM" to find the largest cluster, 2) dump the conformations in 'LOWEST ENERGY DOCKED CONFORMATION from EACH CLUSTER" into an array, 3) use the cluster rank as index to access the correct conformation from the array, 4) combine the ligand conformation with the initial protein conformation into one PDBQT, and finally 5) convert the PDBQT into PDB?

If i am not wrong you want to extract the information from dlg files. The python script will include:

1)Using the glob module get a list of all the files in that folder.

2) it will return you a list of all the files with their path and file name.

3)Then you can parse each of the file name to a file handler using indexing of a list.

4)using regex you can extract the required information. from each file.

I hope you got what i am saying.

Thank You

HI,

Actually I am trying to write the script myself using CSH, I need to know is there any script available

Why CSH? Solution above can do for you. Simply code above and using python shell extract what ever you want to write out.

I am working on three drug targets & CSH is considerably faster

Well, in that case I recommend you include the following instructions:

$mgltoolsdir/write_lowest_energy_ligand.py -f $name.dlg -o $name"_energy".pdbqt

$mgltoolsdir/pdbqt_to_pdb.py -f $name"_energy".pdbqt -o $name"_energy".pdb

mv *"_energy".pdb* ../min_energy/

$mgltoolsdir/write_largest_cluster_ligand.py -t 2.0 -o $name"_clust".pdbqt

$mgltoolsdir/pdbqt_to_pdb.py -f $name"_clust".pdbqt -o $name"_clust".pdb

mv *"_clust".pdb* ../best_clust/

Do you have a script to generate all .dlg results? Because that will be very useful for your analysis

I created a script several years back to do just that. The following csh script will extract all docked conformers from a *.dlg file (generated with Autodock 4.0) as individual PDBQT files and renames so as to keep track of the free energy of binding and the run identifier. The procedure is explained in more detail in my thesis.

Hello,

I want to extract energy from the dock log file, and i used the script getligands ad i modify it to  do that.

but i get this error csplit: {}: integer required between `{' and `}'.