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 Post subject: ADT and pdb data
PostPosted: Tue Jul 21, 2009 11:38 am 
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Dear Dr. Sargis,
I'm interesting to study the interaction between Toxin and protein.
Toxin: Microcystin-LR : http://www.rcsb.org/pdb/explore.do?structureId=1LCM
Protein: Phosphatase protein 1 (PP1): http://www.rcsb.org/pdb/explore.do?structureId=1EVA
I installed ADT and I followed the tutorial how to install autodock4 and autogrid4 for Linux/ubuntu (I moved the binary files to /usr/local/bin).

I'm look for example, how to use pdb data for docking and parse.
I found the example available in Using AutoDock4ADT.pdf tutorial (page 7, Indinavir); but i had some difficult to follow it.

Question is:
How can I use the pdb data for docking Microcystin to PP1?

Thanks


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 Post subject: Re: ADT and pdb data
PostPosted: Tue Jul 21, 2009 5:02 pm 
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mezhoud wrote:
Question is:
How can I use the pdb data for docking Microcystin to PP1?

Dear Mezhoud,

You'll need to convert pdb to pdbqt before using autodock. Please let us know what kind of problems you are experiencing following the tutorial and someone might be able to help you. If your problem is related to (UI) User Interface, then I would recommend PyRx which is user friendly and easier to use and get started with. Good Luck!

_________________
http://pyrx.sf.net


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 Post subject: Re: ADT and pdb data
PostPosted: Wed Jul 22, 2009 6:14 pm 
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Thanks,
I used this link to know how to open pdb file by ADT.
http://www.doe-mbi.ucla.edu/Software/AUTODOCK.html

Thanks


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