ADL: Problems in do_local_only

Czuee Morey czuee_morey at iitb.ac.in
Wed May 14 22:39:30 PDT 2008


Hi everyone,

 I'm trying to do energy minimization of the final docked structure of the
ligand (satisfactorily close to the original crystal structure) in order
to obtain a better conformation using only local search. However, I'm
getting very high binding energies and very different conformatons from
the original docked state. Which parameters can I vary in order to obtain
better results? The dpf file used is as follows

outlev 1                             # diagnostic output level
intelec                              # calculate internal electrostatics
seed pid time                        # seeds for random generator
ligand_types A C OA N P HD           # atoms types in ligand
fld 1RO7_Achain_hyd_2.maps.fld       # grid_data_file
map 1RO7_Achain_hyd_2.A.map          # atom-specific affinity map
map 1RO7_Achain_hyd_2.C.map          # atom-specific affinity map
map 1RO7_Achain_hyd_2.OA.map         # atom-specific affinity map
map 1RO7_Achain_hyd_2.N.map          # atom-specific affinity map
map 1RO7_Achain_hyd_2.P.map          # atom-specific affinity map
map 1RO7_Achain_hyd_2.HD.map         # atom-specific affinity map
elecmap 1RO7_Achain_hyd_2.e.map      # electrostatics map
desolvmap 1RO7_Achain_hyd_2.d.map    # desolvation map
move 1H7T_hyd.016.pdbqt              # small molecule
about 22.9009 -3.0307 12.5923        # small molecule center
tran0 22.901 -3.031 12.592           # initial coordinates/A or random
quat0 random                         # initial quaternion
ndihe 17                             # number of active torsions
dihe0 random                         # initial dihedrals (relative) or random
tstep 2.0                            # translation step/A
qstep 50.0                           # quaternion step/deg
dstep 50.0                           # torsion step/deg
torsdof 17 0.274000                   # torsional degrees of freedom and
coefficient
rmstol 2.0                           # cluster_tolerance/A
extnrg 1000.0                        # external grid energy
e0max 0.0 10000                      # max initial energy; max number of
retries
ga_pop_size 150                      # number of individuals in population
sw_max_its 300                       # iterations of Solis & Wets local
search
sw_max_succ 4                        # consecutive successes before
changing rho
sw_max_fail 4                        # consecutive failures before
changing rho
sw_rho 1.0                           # size of local search space to sample
sw_lb_rho 0.01                       # lower bound on rho
ls_search_freq 0.06                  # probability of performing local
search on individual
set_sw1                              # set the above Solis & Wets parameters
do_local_only 50                     # do this many LS runs
analysis                             # perform a ranked cluster analysis



Czuee Morey,
IIT-Bombay




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