[Dock-fans] Minimisation with DOCK 3.7-beta4

Corey Taylor corey.taylor at uni-marburg.de
Fri Feb 2 06:40:20 PST 2018


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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