Dear AutoDockers
I am using AutoDock Vina for docking. I am successful in running the program and also was able to split the 10 docked conformation using VINA SPLIT script. Now my query is
1. once I run the VinaSplit script, I get 10 different conformations of the same ligand. For example I have attached the first best conformation file namely out_ligand_1.pdbqt . Such file many times contains improper PDB format having ROOT and ENDROOT or sometimes BRANCH and ENDBRANCH or some times both as in the example I have provided.
Such file after merging with protein PDB file wont get opened in 2D interaction analysis tools like LigPlot+. After opening the first confirmation file of ligand in some supported visualizer and then re-saving and re-merging the file into receptor PDB file solves the problem with LigPlot issue.
Now my query is what are that ROOT , ENDROOT or BRANCH , ENDBRANCH. how to convert them to native pdb formats when I have 100s or 1000s of molecules after docking???
2. The merged file when successfully read in LigPlot+and generates the 2D interaction, further the 3D representation obtained from the PyMol sometimes looks like the another file I have attached namely Rg.png. Now my query is what are those extra lines in the pentagon structures?. Why and when do they appear?
Ultimately are there any alternatives that are possible tools and methods that can be more successful that what I am using now???
Please suggest me free softwares.
Hi,
I couldn't remove the line connecting within the five member-ed ring just using MGL tools, but I did some stuff & could resolve the problem.
1. The image 1_PMV_pdbqt.png is the the pdbqt of your original out_ligand_1.pdbqt file & couldn't see the line within, but when I saved out_ligand_1.pdbqt to pdb and opened in PyMOL (out_ligand_1_1.png) could still see that line. The distance between C8 & C12 is 2Angstrom. I checked with another five membered ring structure for reference to know the distance and it is usually 2.2 Angstrom. I am not sure whether the less distance causing the bond formation between them!!!!
2. I checked the pdbqt from AutoDOck vina and also pdbqt generated from PMV after importing to PMV and attached the difference in atom positions.(PDBQT_comparision.png).
But finally using Mercury I could generate the pdb without having the bond between C8 & C12. You could use 00000001.pdb for ligplot+.
Hi,
AutoDock Vina (like AutoDock) works with PDBQT formatted files which differs from PDBs.
To solve your problem you can use:
1) the utility file pdbqt_to_pdb.py
( http://autodock.scripps.edu/faqs-help/faq/where-can-i-find-the-python-scripts-for-preparing-and-analysing-autodock-dockings )
enclosed in the AutoDockTools suite ( MGLTools, http://mgltools.scripps.edu/downloads ):
pdbqt_to_pdb.py -f out_ligand_1.pdbqt -o out_ligand_1.pdb
or,
2) the Open Babel toolbox
( http://openbabel.org/wiki/Get_Open_Babel ):
babel out_ligand_1.pdbqt out_ligand_1.pdb -xrp
You can find more info on how to handle PDBQTs with Open Babel by typing:
babel -L pdbqt
About the PDBQT format, ROOT/ENDROOT or BRANCH/ENDBRANCH have a look here:
http://autodock.scripps.edu/faqs-help/faq/faqsection_view?section=Technical%20Questions
Best.
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