Error with genarating PDBQT for snapshot from MD simulation

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Error with genarating PDBQT for snapshot from MD simulation

Postby aneeshcna » Wed Feb 05, 2014 7:14 am

Dea Users,

I am using PyRx for structrue-based virtual screening. The protein structrue I am using for genarating PDBQT is a MD snapshot ( I am using Amber for simulation). When I use MD snapshot in PDB format and try to genarate PDBQT for the same via File -> load molecule and right-click on entry under Molecules tab and click on AutoDock -> Make Macromolecule menu, PyRx window got hanged with an error, under Logger tab, as shown below..

"Error in : <bound method VSModel. PrepareReceptorMol of..."

What went wrong with the steps?...Is it a problem of added hygrogens in PDB?...How PyRx take care of hydrogens when downloading a protein structure from protein data bank?

What all should I care about when using MD snapshot in PyRx?

Here, I have followed the method described in http://nbcr.ucsd.edu/wiki/index.php/SI2 ... _with_PyRx . The sample run with 2BAT.pdb as mentioned in the website finished successfully.

Many thanks
Aneesh
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Re: Error with genarating PDBQT for snapshot from MD simulat

Postby sargis » Wed Feb 05, 2014 10:56 pm

Dear Aneesh,

Please attach the PDB file you are using. I've just added an FAQ on how to report a bug - http://pyrx.sourceforge.net/faq. Since there are infinitely many possible input files, we can't fix the bug unless we have particular input file you are using.

Thank you for using PyRx!
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Re: Error with genarating PDBQT for snapshot from MD simulat

Postby aneeshcna » Thu Feb 06, 2014 6:09 am

Dear Sargis,

Thanks for the immediate reply. I have attached the PDB file for your close look.

Thanks a lot
Aneesh
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Re: Error with genarating PDBQT for snapshot from MD simulat

Postby sargis » Fri Feb 07, 2014 2:24 am

Dear Aneesh,

Thanks for the PDB file. The MD simulation moved the atoms too far so that there are no longer connected. You can see in the image below that atoms in ASN30 residue, for instance, are disconnected. You'll need to do energy minimization to bring these atoms together before generating PDBQT. Another option is to convert the original PDB into PDBQT, do MD with PDBQT.
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Re: Error with genarating PDBQT for snapshot from MD simulat

Postby aneeshcna » Fri Feb 07, 2014 5:00 am

Thanks for the reply. I have rectified it and now I can generate PDBQT for my protein. I have a quick question here - Auotodock or Autodock Vina, which one will be good option while doing virtual screeing with PyRx?

thanks a lot

Regards
Aneesh
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Re: Error with genarating PDBQT for snapshot from MD simulat

Postby sargis » Fri Feb 07, 2014 5:30 am

You are welcome. Autodock Vina is the default, and most of the time it's a good option for doing virtual screeing with PyRx.
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Re: Error with genarating PDBQT for snapshot from MD simulat

Postby jinzi » Fri Feb 07, 2014 9:46 am

Hi,

I also have the similar problem when I convert the prepare_receptor4.py script with a pqr file from MD simulation.
Can you please have a look?

This is the error I got:
ValueError: Could not find atomic number for 1 1
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