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PyRx Vina- Problem with docking output files
http://mgl.scripps.edu/forum/viewtopic.php?f=27&t=2180
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Author:  Pat [ Tue Dec 04, 2012 4:27 pm ]
Post subject:  PyRx Vina- Problem with docking output files

Hi,

I am new to docking and this forum as well. So, please bear with my novice questions below.

Recently I used PyRx Vina for a docking a crystal ligand (TOK) into the crystal structure of CYP17A1 protein (PDB ID: 3SWZ). PyRx docked it very well with nice overlap with the crystal ligand structure. However, when I checked the crystal structure versus docked structure of this crystal ligand in LigPlot, I see that crystal ligand forms a bond with the heme iron in CYP17A1 protein, while this bond is missing from the docked file for the same ligand.

This is apparently clear when I compare the Mol2 files of the crystal ligand downloaded from PDB versus Mol2 file obtained from the SDF file of the docked ligand-

A) Mol2 file of crystal ligand obtained from PDB website shows following-

@<TRIPOS>MOLECULE
TOK
61 66 0 0 0
SMALL
GASTEIGER

B) Docked Mol2 file of crystal ligand obtained by converting SDF file from PyRx vina output shows following-

@<TRIPOS>MOLECULE
3SWZ-C-TOK_TOK_model_0
31 36 0 0 0
SMALL
GASTEIGER

Can you please help me with this? Why I am unable to reproduce the known hydrogen bond between the crystal ligand and the heme iron in the protein?

Thank you very much for your kind consideration.

Best regards.
Pat

Author:  sargis [ Tue Dec 04, 2012 6:52 pm ]
Post subject:  Re: PyRx Vina- Problem with docking output files

Welcome to this forum and thank you for the post. I recommend attaching screenshots and/or input files to better understand the question. I don't know what this numbers in the mol2 file are, off the top of my head, but PyRx doesn't create or remove bonds after it runs Vina. I've implemented some hydorgen bond visualization in PyRx, but these hydorgen bonds are not saved in the final output.

Hope this clarifies things a bit; maybe someone else will chime in with more info on this..
Thank you for using PyRx!

Author:  Pat [ Thu Dec 06, 2012 1:40 am ]
Post subject:  Re: PyRx Vina- Problem with docking output files

Thank you so much for the prompt reply. Being able to visualize the hydrogen bonds would be really helpful. However, I am not sure how to do that in PyRx. Could you please direct me regarding this?

Thank you again very much for your kind assistance!

Best regards,
Pat

Author:  sargis [ Thu Dec 06, 2012 3:58 am ]
Post subject:  Re: PyRx Vina- Problem with docking output files

You are very welcome Pat. I have implemented this option to visualize the hydrogen bonds in PyRx a while back. This can be accessed by right clicking on a molecule under Molecules tab. This is available in 0.9 version of PyRx. I have made 0.9 binaries for Linux, but unfortunately, I had no time to make these binaries for Windows or Mac.

Thank you and best regards.
Sargis

Attachments:
104-hbonds.png
104-hbonds.png [ 84.61 KiB | Viewed 5536 times ]

Author:  Pat [ Thu Dec 06, 2012 12:14 pm ]
Post subject:  Re: PyRx Vina- Problem with docking output files

Thanks Sargis. This is very useful. I am using windows currently, but I will use Linux and keep you posted.

Thanks again so much!
Pat

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