[Dock-fans] FW: Serious Issues!!!

John Irwin jji at cgl.ucsf.edu
Thu Apr 28 22:50:11 PDT 2005

Hi - Here is another mail from Shuang Luo suggesting some kind of memory
leak (?) that results in different results depending on the order of the
ligands in the input to DOCK5.2. Anyone?


From: shuang luo [mailto:shuang260 at yahoo.com] 
Sent: Thursday, April 28, 2005 1:19 PM
To: John Irwin
Subject: Serious Issues!!!

Dear Dr.Irwin:
Here is one "serious issue" that need your help.
Is there any particular parameter to set when docking a library? I mean
besides those like, multiple_ligands etc.
I found that dock5.2 show different results to ligand regarding to where it
is in the concatenated file. Let me explain in this way, I have 3 ligands,
ligA, ligB and ligC, then concated into one big
mol2 file with the order of ligA-ligB-libC. The docking pose given by
dock5.2 of ligA is the same when dock ligA individually. But the docking
pose is different for ligB and ligC compared to those docking individually.
In other words, if I concatenated the mol2 file in the order of
ligB-ligA-ligC, the pose of ligA is different from the pose when docking
ligA individually. In some case the difference is quite big. 
You can try that for dihydrofolate reductase, 1DF7.pdb, 1DG5.pdb and
1DG7.pdb. This also happen to all the ricin complex I docked.
So obviously, there is some setting that should be reseted after each round
of docking
when docking a library of ligands. I wonder what are they? or maybe it is a
Really looking forward to hearing from you.
With best regards


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