[Dock-fans] Fwd: simplex_random_seed

Trent E. Balius tbalius at aol.com
Thu Nov 12 08:16:27 PST 2015


 Hi,

Q1:  Is there any specificrange number for simplex_random_seed? 

No.  

Q2: Is the zero value reliable or should it be different?

Yes, using zero is the default value.  
Changing this number will give you different results.  

The random seed is used during the minimization at every dock step.   

As is implied in the name the random seed will perturbed your docking
results with some randomness.

Indeed, This may result in a different final pose (fairly, close in Grid Score),
  which is used in the amberscore rescoring step (the differences increase at this step).

I suspect that difference in the final pose is why you are getting such variability in your results.  

Look at the difference in the poses through visual inspection, RMSD calculation, Grid eneregies, 
and AmberScore energies.  
This might help you understand the differences and help you pick which pose you like best.    
 
Q3: Is there any specific reference describing simplex_random_seed?

See the following:

http://dock.compbio.ucsf.edu/DOCK_6/dock6_manual.htm#Minimization
http://www.ncbi.nlm.nih.gov/pubmed/23436713
http://comjnl.oxfordjournals.org/content/7/4/308
http://mailman.docking.org/pipermail/dock-fans/2015-January/003029.html


I hope that this helps,

Trent


======================================
Trent E. Balius, PhD
Postdoc, Shoichet Lab, 
Dept. Pharm. Chem., UCSF
Phone: (415) 514-4253
URL: http://docking.org/~tbalius
======================================

 

 

-----Original Message-----
From: f.mohamadi <f.mohamadi at sci.ui.ac.ir>
To: dock-fans <dock-fans at docking.org>
Sent: Tue, Nov 10, 2015 12:33 am
Subject: [Dock-fans] Fwd: simplex_random_seed




Dear Dock-Fans

I have run several docking tests with different random
seeds (0, 1000,
1500, 2000, 3000, 5000, 10000), I got very different
Amber-Score (from
-29 to -70) which seems a bit strange. Is there any specific
range
number for simplex_random_seed? Is the zero value reliable or should
it
be different?
Is there any specific refference describing
simplex_random_seed?
I would be gratefull if somebody could help me about this
issue.
I also attached my results.

Best
F.M





----- End forwarded
message
-----








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