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 Post subject: Converting to .pdbqt
PostPosted: Wed Jun 27, 2012 11:38 am 
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Hi

Im trying to convert a library of 2million .sdf files to .pdbqt.
I've used openbabel to convert all the .sdf files to .pdb and the prepare_ligand.py command to convert single files to .pdbqt. But as I have a library of 2million files prepare_ligand.py isn't suitable.
I've also used PyRx to do large scale conversions but this begins to lag after ~20 000 conversions and battles to hit 100 000 within a week.

I've also tried openbabel to convert directly from .sdf to .pdbqt but get the error, "Unexpected multi-MODEL input" when doing the docking on vina, even though the file has definitely been split.

Are there any other ways to convert multiple files to .pdbqt.

Thank you


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 Post subject: Re: Converting to .pdbqt
PostPosted: Wed Jun 27, 2012 9:04 pm 
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Hi,

you could try Raccoon.

Stefano


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 Post subject: Re: Converting to .pdbqt
PostPosted: Wed Jun 27, 2012 9:25 pm 
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Thank you! Will give that a try as well.

If anyone else has the same problem as me, I adapted this script to loop through prepare_ligand4.py. Seems to work quite well so far. Hope it can help someone else too.

#! /bin/bash

for f in *.pdb; do
b=`basename $f .pdb`
echo Processing ligand $b
prepare_ligand4.py -l $b.pdb
done

Just make sure prepare_ligand4.py is in your path


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 Post subject: Re: Converting to .pdbqt
PostPosted: Fri Aug 03, 2012 10:49 pm 
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Hi,

I have the same problem. I have close to 2 million ligands form NCI and i converted them to pdb format from sdf using open babel. But when i try to convert them to pdbq using prepare_ligand4.py, using your script, its giving me the error that the prepare command is not found. I have made sure that it is in my path but still it will not work. Any suggestions as to how to get the pdbq files?

Thanks

Shivani


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 Post subject: Re: Converting to .pdbqt
PostPosted: Sun Aug 05, 2012 6:22 pm 
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There's 2 prepare_ligand scripts. Ones from autodock4 (prepare_ligand4.py) and the one from vina (prepare_ligand.py). Sure you have the right one in your path?

The prepare_ligand.py script from vina converts to .pdbq format.....I dont know what this is so I used the prepare_ligand4.py script from autodock4.

If this isnt the prob please let me know.

PS: the tabs in my script were removed when I pasted it, just make sure to put them back (lines between "for..." and "done")


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 Post subject: Re: Converting to .pdbqt
PostPosted: Sun Aug 05, 2012 6:36 pm 
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Also, its a shell script so make sure to save it as name.sh


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 Post subject: Re: Converting to .pdbqt
PostPosted: Mon Aug 06, 2012 4:02 pm 
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I was using the autodock prepare_ligand4.py. I tried tweaking the script a little bit like the making the python script command in the bash script executable with ./ symbol. That worked. I now have the ligand in pdbqt format. also, vina has different scripts. I found it better to use the autodock ones and then use vina for the actual library docking because it gives more accurate results.

Thanks for your help


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 Post subject: Re: Converting to .pdbqt
PostPosted: Wed Aug 15, 2012 9:29 pm 
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Hi,

I have a question. You said that you had a library of 2 million ligands to be docked using vina. How did you do the docking? Did you run 2 million jobs on a server?

~S


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 Post subject: Re: Converting to .pdbqt
PostPosted: Wed Aug 15, 2012 10:05 pm 
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Running it over 30 cpu's on a server.
Took just under 3 weeks.
Also set the exhaustiveness at 4 to speed things up.


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 Post subject: Re: Converting to .pdbqt
PostPosted: Wed Aug 15, 2012 10:11 pm 
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I am trying to do the same. But i cannot run 2 million jobs on the master server directly because there are other people who run it on that server too. So, i was thinking of splitting the ligands so that i can send a script to the queue to different nodes. I haven't worked out how exactly to do this though. do you have any suggestions?

Thanks,

~S


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