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PostPosted: Wed Aug 05, 2009 12:18 am 
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Joined: Tue Aug 04, 2009 2:07 am
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Good to see that an MGL forum has been started. I've been searching this forum and the ADL mailing list, with no apparent answers to my question. I have always used autodock 3 from the command line and organized and prepped my docking output for use in pymol, so it's taken me some time to get accustomed to using ADtools. I have several questions about reclustering, since I run my docking simulations split between several processors on an hpc cluster:

1. I know that it's not possible to use the AD3 version of reclustering, which was to write a cluster.dpf file (about five lines), run AD3, and it would do an analysis with histogram generation and organization of docked results. In ADT, you can recluster several .dlg files under the analysis menu, but when I go to write all conformation coordinates, (say for 1000 runs), ADT write 1000 separate pdbqt files, and the order is the exact order they were read into ADT. Is there any way to organize how ADT writes these pdbqt files so that it is designated by cluster and sub-rank? The alternative is to have to start up ADT each time you want to look at your .dlg files and recluster your results, which is time-consuming at best, extremely annoying at worst.

2. The text file output from ADT reclustering is the closest thing I've seen to the text format of the histogram that appears in clustered results from AD3 .dlg files, but it doesn't give any data that would allow me to quickly locate the xyz coords for a specific conformation (for example, I have 4+ results with a free energy of binding of -14.83 kcal/mol from the reclustering output). I guess this question is tied into my first one, but is there any way to associate the clustering output with the pdbqt files that are written? Better yet, is there some way to concatenate all of the pdbqt files, along with cluster and sub-rank data, into one file?

Sorry for such a long post, but I didn't know how better to put it. Look forward to the answers....

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