ADL: autodock error "no *rigid.HD.map file"

Gauri kamgauri at gmail.com
Thu Sep 16 10:52:01 PDT 2010


I dont have any HD atoms in my ligand but are present in protein.
autogrid runs successfully but autodock fails saying no klm_rigid.HD.map
file
My .gpf file as follows:
.gpf file
npts 60 60 60                        # num.grid points in xyz
gridfld klm_rigid.maps.fld           # grid_data_file
spacing 0.375                        # spacing(A)
receptor_types A C HD N NA OA SA     # receptor atom types
ligand_types A C NA OA N P           # ligand atom types
receptor klm_rigid.pdbqt             # macromolecule
gridcenter 13.812 2.244 -0.346       # xyz-coordinates or auto
smooth 0.5                           # store minimum energy w/in rad(A)
map klm_rigid.A.map                  # atom-specific affinity map
map klm_rigid.C.map                  # atom-specific affinity map
map klm_rigid.NA.map                 # atom-specific affinity map
map klm_rigid.OA.map                 # atom-specific affinity map
map klm_rigid.N.map                  # atom-specific affinity map
map klm_rigid.P.map                  # atom-specific affinity map
elecmap klm_rigid.e.map              # electrostatic potential map
dsolvmap klm_rigid.d.map              # desolvation potential map
dielectric -0.1465                   # <0, AD4 distance-dep.diel;>0,
constant

My .dpf file is:
autodock_parameter_version 4.2       # used by autodock to validate
parameter set
outlev 1                             # diagnostic output level
intelec                              # calculate internal electrostatics
seed pid time                        # seeds for random generator
ligand_types A C NA OA N P HD        # atoms types in ligand
fld klm_rigid.maps.fld               # grid_data_file
map klm_rigid.A.map                  # atom-specific affinity map
map klm_rigid.C.map                  # atom-specific affinity map
map klm_rigid.NA.map                 # atom-specific affinity map
map klm_rigid.OA.map                 # atom-specific affinity map
map klm_rigid.N.map                  # atom-specific affinity map
map klm_rigid.P.map                  # atom-specific affinity map
map klm_rigid.HD.map                 # atom-specific affinity map
elecmap klm_rigid.e.map              # electrostatics map
desolvmap klm_rigid.d.map            # desolvation map
move NAD.pdbqt                       # small molecule
flexres klm_flex.pdbqt                  # file containing flexible residues
about -0.3045 -15.5513 15.1056       # small molecule center
tran0 random                         # initial coordinates/A or random
axisangle0 random                    # initial orientation
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 11                            # torsional degrees of freedom
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
ga_num_evals 2500000                 # maximum number of energy evaluations
ga_num_generations 27000             # maximum number of generations
ga_elitism 1                         # number of top individuals to survive
to next generation
ga_mutation_rate 0.02                # rate of gene mutation
ga_crossover_rate 0.8                # rate of crossover
ga_window_size 10                    # 
ga_cauchy_alpha 0.0                  # Alpha parameter of Cauchy
distribution
ga_cauchy_beta 1.0                   # Beta parameter Cauchy distribution
set_ga                               # set the above parameters for GA or
LGA
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_psw1                             # set the above pseudo-Solis & Wets
parameters
unbound_model bound                  # state of unbound ligand
ga_run 10                            # do this many hybrid GA-LS runs
analysis                             # perform a ranked cluster analysis

Any suggestions are welcomed.
thanks 
Gauri
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