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AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
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 Post subject: Re: Converting to .pdbqt
PostPosted: Thu Aug 16, 2012 1:06 pm 
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I split it into 15 different jobs and then ran the vina_screen_local.sh script in each job. Luckily the the ZINC database did the split for me, but you can try fpart (http://sourceforge.net/projects/fpart/) to split the list of ligands into separate folders. Fpart only puts out a list of names so you'll have to write a script to copy the contents of the list...I used an awk script.

I would also advise splitting the 2mil into more than 15 separate jobs.....vina wont use all the cpu's its given if the exhaustiveness is low so split into smaller jobs with 2cpu's per job.

Let me know if this helps or not!


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 Post subject: Re: Converting to .pdbqt
PostPosted: Fri Sep 07, 2012 7:20 pm 
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Joined: Fri Aug 03, 2012 10:43 pm
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Hi,

Your answer was very helpful. I wrote a script to divide ligand files into 50 jobs and then ran vina on them. The docking got done very fast.

Thanks!


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