ADL: Solvation Parameters
zgleo at tom.com
Sun Sep 12 05:01:22 PDT 2004
Dear Garrett M. Morris£¬
The setting of "rmstol" doesn't work in fact. Whatever value you change the setting to, autodock always uses 1 Angstrom as the real tolerance RMSD. Maybe it's a small bug occurring during the read of the dpf file.
>This is a very good question.
>You can be pretty certain if you obtain just one cluster at the end of
>the docking; 10 dockings per compound may be enough, but you are doing
>very "deep" dockings, at 50 million evals. You might like to try 100
>dockings at 5 million evals, to compare the how best to "spend" the
>same number of energy evaluations ("evals"). See if you get reasonable
>docked conformations at the end of each kind of docking; 100 dockings
>is more likely to give you better clustering statistics. If you start
>with random number generator seeds that are dependent on the time and
>process id (pid) of your docking (this is the deafult behaviour for
>AutoDock scripts like mkdpf3 and ADT), then you should get different
>results each time: remember that AutoDock's search methods, SA, GA and
>LGA, are all stochastic search methods, which means the outcome will
>vary depending on the random numbers generated during the docking.
>You can be confident of convergence if you obtain the same
>conformations frequently or even always, and this will be reflected in
>the conformational clustering in the histogram at the end of the DLG
>(docking log file). The clustering depends on the size of your ligand
>and the rmsd tolerance you use, but it is best to use an "rmstol" of
>about 2 Angsroms for your clustering.
>I hope this helps,
Chinese Academy of Science
zgleo at tom.com
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