[Dock-fans] Posible problem with the restrained min & Fwd: Uncaught bounce notification

Trent E. Balius tbalius at aol.com
Tue Sep 1 10:37:44 PDT 2015


 Hi,
Thanks for pointing this out to us. 
I am forwarding this to the dock-fans so that this is brought to others attention. 
I see why you thought that this might be  a bug, but I am not sure it is.

I think that "ref_mol" is a molecule conformation generated during simplex minimization and

"rmsd_ref" is the conformation to which we restrain the poses during the minimization.   

I think that the code is ok. 
Perhaps, other on the list can verify that I am right.

Thanks,
Trent

 

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

 

 

-----Original Message-----
From: John Irwin <jir322 at gmail.com>
To: Trent Balius <tbalius at aol.com>
Sent: Mon, Aug 31, 2015 9:46 pm
Subject: Fwd: Uncaught bounce notification


Hi Trent

This is communication erroneously to dock_industry. Can you
either
forward to dock-fans, or answer directly, or possibly
both?

Thanks

John



---------- Forwarded message ----------
From: 
<mailman-bounces at mailman.bkslab.org>
Date: Mon, Aug 31, 2015 at 6:49
PM
Subject: Uncaught bounce notification
To:
dock_industry-owner at mailman.bkslab.org


The attached message was received as
a bounce, but either the bounce
format was not recognized, or no member
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from it.  This mailing list has been configured to
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For more
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----------
Forwarded message ----------
From: <liao149115 at sina.com>
To:
dock_industry-bounces <dock_industry-bounces at mailman.bkslab.org>
Cc:
Date:
Tue, 01 Sep 2015 11:01:08 +0800
Subject: The code problem of Dock

Dear DOCK
Team,


We are reading the source code of DOCK 6.6. We have a doubt in
the
following code.



Simplex_Minimizer::simplex_minimize(...)   -  (in
the file
src/dock/simple.cpp)

----------------------------------------------------------------------------------

...


if (simplex_score (score, ref_mol, tmp_mol, vertex, trans_step_size,

        
rot_step_size, tors_step_size)) {



                     if
(restrained_min){

                         Econstraint =
coefficient_restraint *
calc_active_rmsd2(rmsd_ref,tmp_mol);

               
} else

                         Econstraint = 0.0;


                    
y[i] = tmp_mol.current_score + tmp_mol.internal_energy

                      
+ Econstraint;


                } else {


                    // store
best scoring vertex

                    for (x = 0; x < size; x++)

       
vertex[x] = p[ilo][x];


                    //optimum =
ref_mol.current_score;

                    if (restrained_min){

          
Econstraint = coefficient_restraint *
calc_active_rmsd2(rmsd_ref,ref_mol);

 
} else

                         Econstraint = 0.0;


                   
optimum = ref_mol.current_score +
ref_mol.internal_energy //trent balius
2008-12-05

                              +
Econstraint;

...

----------------------------------------------------------------------------------


Should
the bold 'ref_mol' be 'tmp_mol'?


SIncerely,

Chenzhi Liao, Junshi
Chen

University of Science and Technology of China

 
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