冰晶石 发表于 2012-12-2 13:08:35

求助autodock 金属配体问题

autodock里面，ligand 含金属，不知道如何手动加电荷，谁能指点一下，我查了各种网上说法，可能我改得不对，改完以后 run dock 被提示 Must Specify a docking parameter file（.dpf）

冰晶石 发表于 2012-12-2 13:10:29

其它论坛有 讨论 http://simulation.5d6d.net/thread-38064-1-1.html

最后的解决办法是在。pdbqt文件中，手动添加。还好，我只需要在受体文件中添加～～～现在要是在配体中添加，那可就有的活干了.

http://autodock.1369657.n2.nabbl ... quot-td4628025.html
One solution could be to calculate the partial charges in a different way by using
semi-empirical or QM packages (MOPAC, Gaussian, Gamess...), save the molecule as Mol2 and
use the prepare_ligand4.py script (that comes with ADT) with the "-C" or "-p" options to
preserve all the charges or only the one in your atom type, respectively.

Another solution could be to edit the PDBQT ligand file and manually add a "reasonable"
charge, while keeping the total molecular charge as integer (0.0, +1.0, -2.0, ...)

Hope this helps,

冰晶石 发表于 2012-12-2 15:25:55

解决办法
群里的 SCAU-viger 和川大-灰太狼 都说了如下办法
1. 将金属的参数写入AD4_parameters.dat文件中，并将该文件copy到计算目录下（即配合物、大分子所在文件夹）。
ps：金属的参数在官网有，应该是指我们qq群论坛
“关于Autodock 添加非默认原子类型力场参数的讨论”

需要添加的原子力场如下：

atom_par C 4.00 0.150 33.5103 -0.00143 0.0 0.0 0 -1 -1 0 # Non H-bonding
atom_par A 4.00 0.150 33.5103 -0.00052 0.0 0.0 0 -1 -1 0 # Non H-bonding
atom_par N 3.50 0.160 22.4493 -0.00162 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par NA 3.50 0.160 22.4493 -0.00162 1.9 5.0 4 -1 -1 1 # Acceptor 1 H-bond
atom_par NS 3.50 0.160 22.4493 -0.00162 1.9 5.0 3 -1 -1 1 # Acceptor S Spherical
atom_par OA 3.20 0.200 17.1573 -0.00251 1.9 5.0 3 -1 -1 2 # Acceptor 2 H-bonds
atom_par OS 3.20 0.200 17.1573 -0.00251 1.9 5.0 3 -1 -1 2 # Acceptor S Spherical
atom_par SA 4.00 0.200 33.5103 -0.00214 2.5 1.0 5 -1 -1 6 # Acceptor 2 H-bonds
atom_par S 4.00 0.200 33.5103 -0.00214 0.0 0.0 0 -1 -1 6 # Non H-bonding
atom_par H 2.00 0.020 0.0000 0.00051 0.0 0.0 0 -1 -1 3 # Non H-bonding
atom_par HD 2.00 0.020 0.0000 0.00051 0.0 0.0 2 -1 -1 3 # Donor 1 H-bond
atom_par HS 2.00 0.020 0.0000 0.00051 0.0 0.0 1 -1 -1 3 # Donor S Spherical
atom_par P 4.20 0.200 38.7924 -0.00110 0.0 0.0 0 -1 -1 5 # Non H-bonding
atom_par Br 4.33 0.389 42.5661 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par BR 4.33 0.389 42.5661 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par Ca 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par CA 1.98 0.550 2.7700 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par Cl 4.09 0.276 35.8235 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding
atom_par CL 4.09 0.276 35.8235 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding
atom_par F 3.09 0.080 15.4480 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding
atom_par Fe 1.30 0.010 1.8400 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par FE 1.30 0.010 1.8400 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par I 4.72 0.550 55.0585 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-binding
atom_par Mg 1.30 0.875 1.5600 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par MG 1.30 0.875 1.5600 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par Mn 1.30 0.875 2.1400 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par MN 1.30 0.875 2.1400 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par Zn 1.48 0.550 1.7000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par ZN 1.48 0.550 1.7000 -0.00110 0.0 0.0 0 -1 -1 4 # Non H-bonding
atom_par He 2.36 0.056 15.240 -0.00110 0.0 0.0 0 -1 -1 0 # Non H-bonding
atom_par Li 2.45 0.025 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Be 2.76 0.085 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par B 4.08 0.180 12.052 -0.00110 0.0 0.0 0 -1 -1 0 # Non H-bonding
atom_par Ne 3.24 0.042 15.440 -0.00110 0.0 0.0 0 -1 -1 0 # Non H-bonding
atom_par Na 3.98 0.030 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Al 4.49 0.505 11.278 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Si 4.30 0.402 12.175 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par K 3.81 0.035 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Sc 3.30 0.019 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ti 3.18 0.017 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par V 3.14 0.016 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Co 2.87 0.014 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ni 2.83 0.015 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Cu 3.50 0.005 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ga 4.38 0.415 11.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ge 4.28 0.379 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par As 4.23 0.309 13.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Se 4.21 0.291 14.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Kr 4.14 0.220 16.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Rb 4.11 0.040 12.000 -0.00110 0.0 0.0 0 -1 -1 2 # Non H-bonding
atom_par Sr 3.64 0.235 12.000 -0.00110 0.0 0.0 0 -1 -1 2 # Non H-bonding
atom_par Y 3.35 0.072 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Zr 3.12 0.069 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Nb 3.17 0.059 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Mo 3.05 0.056 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Tc 3.00 0.048 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ru 2.96 0.056 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Rh 2.93 0.053 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Pd 1.34 0.048 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ag 3.15 0.036 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Cd 2.85 0.228 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par In 4.46 0.599 11.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Sn 4.39 0.567 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Sb 4.42 0.449 13.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Te 4.47 0.398 14.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Xe 4.40 0.332 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Cs 4.52 0.045 12.000 -0.00110 0.0 0.0 0 -1 -1 2 # Non H-bonding
atom_par Ba 3.70 0.364 12.000 -0.00110 0.0 0.0 0 -1 -1 2 # Non H-bonding
atom_par La 3.52 0.017 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ce 3.56 0.013 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Pr 3.61 0.010 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Nd 3.58 0.010 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Pm 3.55 0.009 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Sm 3.52 0.008 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Eu 3.49 0.008 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Gd 3.37 0.009 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Tb 3.45 0.007 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Dy 3.43 0.007 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ho 3.41 0.007 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Er 3.39 0.007 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Tm 3.37 0.006 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Yb 3.36 0.228 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Lu 3.64 0.041 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Hf 3.41 0.072 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ta 3.71 0.081 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par W 3.07 0.067 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Re 2.95 0.066 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Os 3.12 0.120 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Ir 2.84 0.073 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Pt 2.75 0.080 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Au 3.29 0.039 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Hg 2.71 0.385 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Tl 4.35 0.680 11.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Pb 4.30 0.663 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Bi 4.37 0.518 13.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Po 4.71 0.325 14.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par At 4.75 0.284 15.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Rn 4.77 0.248 16.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Fr 4.90 0.050 12.000 -0.00110 0.0 0.0 0 -1 -1 2 # Non H-bonding
atom_par Ra 3.68 0.404 12.000 -0.00110 0.0 0.0 0 -1 -1 2 # Non H-bonding
atom_par Ac 3.48 0.033 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Th 3.40 0.026 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Pa 3.42 0.022 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par U 3.40 0.022 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Np 3.42 0.019 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Pu 3.42 0.016 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Am 3.38 0.014 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Cm 3.33 0.014 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Bk 3.34 0.013 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Cf 3.31 0.013 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par E 3.30 0.012 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding
atom_par Fm 3.29 0.012 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding

2. 然后在gpf、dpf文件中添加：
parameter_file AD4_parameters.dat    # force field default parameter file
我是win下操作的，所以是从 grid -> other opertion ->edit paramter 里面导入
至于dpf文件添加，我还不会，所以先整理到这吧
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