[Dock-fans] minimization options and the florida weather

Terry Lang terry at cgl.ucsf.edu
Wed Mar 2 11:57:47 PST 2005


Dear Jose,

   First of all, version 5.1.0 is outdated.  We currently are in version 
5.1.1 and will be releasing version 5.2 in the next few weeks.  I would 
strongly recommend getting the newer versions because, in addition to the 
new capabilities, these version contain important bug fixes.  Most of the 
concerns that you have listed here are fixed in the newer versions.


>Is there a mistake in that document?
>
>On page 15, at the top, where minimize_final_pose_rigid is listed twice. 
>It seems the flag for torsional minimizatin would be different...

Yes, this is a typo.  The second parameter should read 
"minimize_final_pose_torsions."

>If I am NOT searching conformations, will "minimize_final_pose_complete" 
>work for the orientation search? (i.e. will dock minimize torsion, or only 
>rigid bodies?) (page15)

The "minimize_final_pose_complete" will perform a minimization on 
rotational, translational, and torsional degrees of freedom.  It should 
work on any molecule, even if orientation has not been performed.

>Would it be ok to say "minimize_ligand" is the switch (literally a flag) 
>that just tells dock to ask me for all of the other parameters? And that 
>"it doesn't do anything in itself"

Yes, that is correct.

>Do these behave any differently if I am NOT searching conformations
>
>Minimize_rigid_anchor
>
>Minimize_final_pose
>
>(am I right to assume minimize_layer_growth is not applicable for 
>orientational searches only?)
>
>the reason these confuse me is that DOCK asks me for them even though 
>flexible ligands is off.

The minimize_rigid_anchor and minimize_layer_growth options are for 
flexible docking.  The minimize_final_pose works for rigid docking and for 
the final pose in flexible docking after the growth has been completed.  I 
can understand why this is confusing and we will probably try to fix this 
in version 5.3.

>About that document, is that the latest manual, or is there a more 
>extensive description of DOCK5 (I already have read and have with me the 
>dock4 manual)

>One last more general question, about the rank_ligands parameter, is this 
>supposed to spit out a list of molecules (e.g. oriented and scored) in 
>increasing order from best score to worse? I set max_ranked ligands to 
>100, but in the _ranked.mol2 outputs I must have the whole database 
>because clearly i have more than 100 molecules scored...and not in order...

See the first paragraph for the answers to these questions.

>Thanks in advance for any answers
>
>Jose
>
>Graduate Student
>
> From the University of Florida
>
>PS: It's going to be in the 30s tonight...oh my God! it's going to be 
>cold! (just wanted to tease the dockfans upnorth. Ahem!
>
>
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P. Therese (Downing) Lang
Kuntz and James Labs
UCSF - CCB Graduate Program
Phone:  (415)476-3986
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