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.

Thank you Ballante. Thanks a lot