Run Autodock 最后一步闪退，求助
求教大神：从 PDB 库中下载的受体和配体，用autodock 对接结合能基本在 -7.8~-7.3 之间，
但是自己画的配体 3D结构 在经过MM2 优化，存成 .pdb，同受体对接在最后一步总是闪退，提示
“autodock needs the extension of the docking parameter file to be “.dpf”，不知何故？ 存盘的路径和文件名均为英文
你的.dpf文件有产生吗？ 有产生的
如下：
parameter_file AD4_parameters.dat # force field default parameter file
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 HD OA N # atoms types in ligand
fld 2NPPPRO.maps.fld # grid_data_file
map 2NPPPRO.A.map # atom-specific affinity map
map 2NPPPRO.C.map # atom-specific affinity map
map 2NPPPRO.HD.map # atom-specific affinity map
map 2NPPPRO.OA.map # atom-specific affinity map
map 2NPPPRO.N.map # atom-specific affinity map
elecmap 2NPPPRO.e.map # electrostatics map
desolvmap 2NPPPRO.d.map # desolvation map
move ALX LR.pdbqt # small molecule
about -0.0026 0.3593 0.108 # small molecule center
tran0 random # initial coordinates/A or random
quaternion0 random # initial orientation
dihe0 random # initial dihedrals (relative) or random
torsdof 17 # 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 100 # do this many hybrid GA-LS runs
analysis # perform a ranked cluster analysis
QQ 有建议：试试在 Edit dpf中输入路径，保存再看看。 请问如何输入路径，能否给个例子
我试着MM2优化好了，保存成.pdb时， chembio3D 提示存盘时，可能会有损失（not a native format ，some information 在存盘时可能会丢失）
我试着用Gaussian 继续优化，然后将得到的 OUT文件，用Gview 打开后存成 .pdb 格式，没在提示可能会有信息损失，但是 用正常的对接还是不行（从 PDB 库中下载的受体和配体确实每次都成功的） 我试了以前画的其他配体结构（已优化），对接没问题。 估计是这次的结构不对头，操作没问题，谢谢！
页:
[1]