[Dock-fans] Minimisation with DOCK 3.7-beta4

Trent E. Balius tbalius at aol.com
Fri Feb 2 08:16:05 PST 2018


Hi Corey,

Later versions of DOCK3.7 do have the minimization implemented: for example, the current release DOCK3.7.1rc1. 

Please download the new version and try it.

Here is some a helpful wiki page:

http://wiki.bkslab.org/index.php/DOCK3.7_INDOCK_Minimization_Parameter

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: Corey Taylor <corey.taylor at uni-marburg.de>
To: dock-fans <dock-fans at docking.org>
Sent: Fri, Feb 2, 2018 6:40 am
Subject: [Dock-fans] Minimisation with DOCK 3.7-beta4


Hi all,

So I've tried to activate minimisation in our version of DOCK (DOCK v.
3.7, compiled 20160520) and tried using the INDOCK section as at
http://wiki.bkslab.org/index.php/DOCK3.7_INDOCK_Minimization_Parameter :

#####################################################
# MINIMIZATION
minimize yes
sim_itmax 500
sim_trnstep 0.2
sim_rotstep 5.0
sim_need_to_restart 1.0
sim_cnvrge 0.1
min_cut 1.0e15
iseed 777


I get errors in the OUTDOCK:

ERROR ---> Could not parse all INDOCK parameters!
ERROR ---> stops

Of course the minimisation parameters for DOCK 3.6 look quite different:

###############################################################################
# MINIMIZATION
#
minimize yes
minimization_max 1.0e15
check_degeneracy no
simplex_iterations 250
simplex_convergence 0.1
simplex_restart 1.0
simplex_initial_translation 0.2
simplex_initial_rotation 5.0
#

These don't work with DOCK 3.7 as they're deprecated according to the
OUTDOCK.

Were there slightly different parameters for this version of DOCK 3.7 vs
what was released later or was minimization just not activated at all in
this version? Or would this just be more easily solved by just upgrading
to a more recent version perhaps? If so, can I get a link or should I
just submit data via the dock license application form
(http://dock.compbio.ucsf.edu/Online_Licensing/dock_license_application.html)?

Thanks guys,

--
Corey Taylor
Kolb Lab
Institute of Pharmaceutical Chemistry
Philipps-University Marburg
Marbacher Weg 6
35032 Marburg
Germany

Mailto: corey.taylor at uni-marburg.de
Ph: +49 6421 28 21351
Web: http://www.kolblab.org/taylor.html

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