Using PyRx with AutoDock

Python Prescription - Virtual Screening Tool

Moderator: sargis

Using PyRx with AutoDock

Postby olivia.newman » Fri Mar 01, 2013 6:28 pm

I want to prepare a macromolecule in AutoDock but dock it in PyRx. I was able to do this in the 4.0 version, but now I have AutoDock 4.2 and while their is a general tutorial for it, it is not very specific about each step to preparing a macromolecule to be placed in PyRx. What can I look at to help me figure this out?

Thank you in advance for your help.
User avatar
olivia.newman
Millimolar User
Millimolar User
 
Posts: 4
Joined: Fri Oct 12, 2012 6:20 pm

Re: Using PyRx with AutoDock

Postby sargis » Sat Mar 02, 2013 5:09 am

Thank you for the post. I haven't had a chance to write a documentation about this, but as far as I know, preparing a macromolecule hasn't changed between AutoDock version 4.0 and 4.2. Perhaps if you can provide more specifics about which version of PyRx you are using and on which OS (Linux, Windows or Mac), I'll be able to help you to figure this out.

Thank you for using PyRx!
User avatar
sargis
Picomolar User
Picomolar User
 
Posts: 479
Joined: Fri Oct 17, 2008 10:39 pm

Re: Using PyRx with AutoDock

Postby olivia.newman » Sun Mar 10, 2013 9:26 pm

Sorry for getting back to you so late. I am using windows but honestly I'm not sure how to tell what version of PyRx it is because it is a school computer and someone else in charge of the computers downloaded it for me. I noticed that most of everything is the same but I am just having trouble saving the macromolecule in autodock. When I click "write PDBQT" it comes up with an error about polar hydrogens that are missing even though I added polar hydrogens so I don't know how to fix that. It did not do that with the old version and the same macromolecule.
User avatar
olivia.newman
Millimolar User
Millimolar User
 
Posts: 4
Joined: Fri Oct 12, 2012 6:20 pm

Re: Using PyRx with AutoDock

Postby olivia.newman » Sun Mar 10, 2013 9:59 pm

I think I figured it out! I still have one question though. I saved two different kinds of the macromolecule. In both I added Kollman charges, computed Gasteiger charges, and assigned AD4 types before I saved it as a document. But in one of them I added all hydrogens first and in the other I didn't. Which one should I use? I'm guessing the one with hydrogens because it says that in the tutorial, but I was just shocked at how much it changed the molecule when I added them and it seems like so many that I was worried it will not give me the right results if the molecule is different.
User avatar
olivia.newman
Millimolar User
Millimolar User
 
Posts: 4
Joined: Fri Oct 12, 2012 6:20 pm

Re: Using PyRx with AutoDock

Postby sargis » Mon Mar 11, 2013 8:59 pm

Great, I'm glad you figured it out. Kudos to the person installed PyRx on your computer; very smart move. I haven't had a chance to make any updates to Windows installer for years - http://sourceforge.net/apps/trac/pyrx/roadmap

That's why there might be bugs in Windows version that might have already been fixed in the latest Linux version of PyRx.

Regarding the question about adding hydrogens: yes, please do add hydrogens before making pbqt. Ask 3 scientists how to get the right results in docking and you will get five different answers.
User avatar
sargis
Picomolar User
Picomolar User
 
Posts: 479
Joined: Fri Oct 17, 2008 10:39 pm

Re: Using PyRx with AutoDock

Postby olivia.newman » Mon Mar 11, 2013 11:41 pm

Oh! that explains why I had trouble with it on my laptop and needed them to install it on the school computer.
haha Ok thank you so much for your help!
User avatar
olivia.newman
Millimolar User
Millimolar User
 
Posts: 4
Joined: Fri Oct 12, 2012 6:20 pm


Return to PyRx

Who is online

Users browsing this forum: No registered users and 1 guest

cron