Prepare Macromolecules for Vina

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Prepare Macromolecules for Vina

Postby Vaniss Tan » Sat Nov 08, 2014 2:53 am

Hi Dr Sargis,
I had installed PyRx version 0.8 in window 8, 64-bit operating system, x64-based processor and with python 2.7.8 ,microsoft visual C++ 2012.
Now, I am preparing the macromolecule, as I know PyRx do remove water molecules before converting it to pdbqt format, but may i know whether Pyrx also add hydrogen to the macromolecule? As I saw some of the research paper states that it is necessary to add hygrogen to the macromolecule before doing docking. Thank you.

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Vaniss
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Re: Prepare Macromolecules for Vina

Postby sargis » Sat Nov 08, 2014 5:00 pm

Hi Vaniss,

Thank you for the message. PyRx does add hydrogen to the macromolecule when converting it to pdbqt format. It's using AD4ReceptorPreparation which has nice defaults.

Thank you for using PyRx!

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Sargis
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Re: Prepare Macromolecules for Vina

Postby Vaniss Tan » Mon Nov 10, 2014 8:23 am

Hi Dr Sargis,
Thank you for your reply. you did solve my problem. Now I can run Autodock Vina and got my result. but may I know how can i download the interaction of protein-ligand file? As i know, we can download the result table in CSV, but if i want to visualize the interaction of protein-ligand using Pymol, how can I download the structure file?
Thank you.

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vaniss
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