ADL: parameters for trajectory output during SA dockings

dengguowei dgwei at pku.edu.cn
Fri Apr 27 08:29:44 PDT 2007


hi everyone:

     I plan to sample the states during a docking and output to a
trajectory file. The dpf file of mine is as followed:
     But i can't get the trajectory file that contain the state
variable.
   
     If someone know the reason, please tell me, and i am worried about
it for along time
     Thank you very much!

         
###############dpf file###############
outlev 1                             # diagnostic output level
seed pid                        # seeds for random generator
types CANOSH                         # atom type names
fld 1y6q_d_h.maps.fld                # grid_data_file
map 1y6q_d_h.C.map                   # atom-specific affinity map
map 1y6q_d_h.A.map                   # atom-specific affinity map
map 1y6q_d_h.N.map                   # atom-specific affinity map
map 1y6q_d_h.O.map                   # atom-specific affinity map
map 1y6q_d_h.S.map                   # atom-specific affinity map
map 1y6q_d_h.H.map                   # atom-specific affinity map
map 1y6q_d_h.e.map                   # electrostatics map
move 1y6q_lig_sy.out.pdbq            # small molecule
about 56.0711 73.0632 20.5413        # small molecule center
tran0 random                         # initial coordinates/A or random
quat0 random                         # initial quaternion
ndihe 6                              # 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 4 0.3113                     # torsional degrees of freedom and
coeffiecent
intnbp_r_eps  4.00 0.0222750 12 6    # C-C lj
intnbp_r_eps  4.00 0.0222750 12 6    # C-A lj
intnbp_r_eps  3.75 0.0230026 12 6    # C-N lj
intnbp_r_eps  3.60 0.0257202 12 6    # C-O lj
intnbp_r_eps  4.00 0.0257202 12 6    # C-S lj
intnbp_r_eps  3.00 0.0081378 12 6    # C-H lj
intnbp_r_eps  4.00 0.0222750 12 6    # A-A lj
intnbp_r_eps  3.75 0.0230026 12 6    # A-N lj
intnbp_r_eps  3.60 0.0257202 12 6    # A-O lj
intnbp_r_eps  4.00 0.0257202 12 6    # A-S lj
intnbp_r_eps  3.00 0.0081378 12 6    # A-H lj
intnbp_r_eps  3.50 0.0237600 12 6    # N-N lj
intnbp_r_eps  3.35 0.0265667 12 6    # N-O lj
intnbp_r_eps  3.75 0.0265667 12 6    # N-S lj
intnbp_r_eps  2.75 0.0084051 12 6    # N-H lj
intnbp_r_eps  3.20 0.0297000 12 6    # O-O lj
intnbp_r_eps  3.60 0.0297000 12 6    # O-S lj
intnbp_r_eps  2.60 0.0093852 12 6    # O-H lj
intnbp_r_eps  4.00 0.0297000 12 6    # S-S lj
intnbp_r_eps  3.00 0.0093852 12 6    # S-H lj
intnbp_r_eps  2.00 0.0029700 12 6    # H-H lj
#
rmstol 1.0                           # cluster_tolerance/A

trjfrq 7500
trjbeg 45
trjend 50
trjout check2.trj
trjsel E

extnrg 1000.0                        # external grid energy
e0max 0.0 10000                      # max initial energy; max number of
retries
rt0 500.0                           # initial annealing temperature
(times gas constant)
linear_schedule                      # use linear, arithmetic
temperature reduction
rtrf 0.95                            # annealing temperature reduction
factor
trnrf 1.0                            # per cycle reduction factor for
translation
quarf 1.0                            # per cycle reduction factor for
quaternions
dihrf 1.0                            # per cycle reduction factor for
dihedrals
runs 10                              #
cycles 50                            # number of temperature reduction
cycles
accs 100                             # maximum number of accepted steps
per cycle
rejs 100                             # maximum number of rejected steps
per cycle
select m                             # state selection flag: (m)inimum
or (l)ast state
simanneal                            # do as many SA runs as set by runs
keyword above
analysis                             # perform a ranked cluster analysis


#############the check2.trj############
ntorsions 6
run 1
ntorsions 6
run 2
ntorsions 6
run 3
ntorsions 6
run 4
ntorsions 6
run 5
ntorsions 6
run 6
ntorsions 6
run 7
ntorsions 6
run 8
ntorsions 6
run 9
ntorsions 6
run 10




 



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