Autodock 默认的原子类型及力场添加操作

MYM 发表于 2014-2-27 20:24:44

Autodock 默认的原子类型及力场添加操作

灰太狼撰写，在此转发。
Autodock 默认的原子类型及力场添加操作：

比如做含Ni原子的蛋白，添加Ni的力场参数到 AD4_parameters.dat 文件： atom_par Ni 2.83 0.015 12.000 -0.00110 0.0 0.0 0 -1 -1 1 # Non H-bonding 然后在做grid的时候添加 parameter_file AD4_parameters.dat 到.gpf 文件的第一行。等待grid计算完毕后，在生成的dpf文件里添加 parameter_file AD4_parameters.dat 在第一行。进行docking，得到结果。

注意：a. Cu离子参数写入AD4_parameters.dat文件，再将此文件copy到计算目录下
   b. 在gpf、dpf文件中加入以下字段（指定参数文件）：
parameter_file AD4_parameters.dat # force field default parameter file

Autodock 默认的原子类型及力场信息如下：
# $Id: AD4_parameters.dat,v 1.14 2007/04/27 06:01:47 garrett Exp $
#
# AutoDock
#
# Copyright (C) 1989-2007,Garrett M. Morris, David S. Goodsell, Ruth Huey, Arthur J. Olson,
# All Rights Reserved.
#
# AutoDock is a Trade Mark of The Scripps Research Institute.
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA02110-1301, USA.

# AutoDock Linear Free Energy Model Coefficients and Energetic Parameters
#                      Version 1.0
#                   $Revision: 1.14 $

# AutoDock 4 free energy coefficients with respect to original (AD2) energetic parameters
#
#             Free Energy Coefficient
#             ------
FE_coeff_vdW 0.1560
FE_coeff_hbond0.0974
FE_coeff_estat0.1465
FE_coeff_desolv 0.1159
FE_coeff_tors 0.2744

# AutoDock 4 Energy Parameters

# - Atomic solvation volumes and parameters
# - Unweighted vdW and Unweighted H-bond Well Depths
#
# - Atom Types
# - Rii = sum of vdW radii of two like atoms (in Angstrom)
# - epsii = vdW well depth (in Kcal/mol)
# - vol = atomic solvation volume (in Angstrom^3)
# - solpar = atomic solvation parameter
# - Rij_hb = H-bond radius of the heteroatom in contact with a hydrogen (in Angstrom)
# - epsij_hb = well depth of H-bond (in Kcal/mol)
# - hbond = integer indicating type of H-bonding atom (0=no H-bond)
# - rec_index = initialised to -1, but later on holds count of how many of this atom type are in receptor
# - map_index = initialised to -1, but later on holds the index of the AutoGrid map
# - bond_index = used in AutoDock to detect bonds; see "mdist.h", enum {C,N,O,H,XX,P,S}
#
# - To obtain the Rij value for non H-bonding atoms, calculate the
#    arithmetic mean of the Rii values for the two atom types.
#    Rij = (Rii + Rjj) / 2
#
# - To obtain the epsij value for non H-bonding atoms, calculate the
#    geometric mean of the epsii values for the two atom types.
#    epsij = sqrt( epsii * epsjj )
#
# - Note that the Rij_hb value is non-zero for heteroatoms only, and zero for H atoms;
#    to obtain the length of an H-bond, look up Rij_hb for the heteroatom only;
#    this is combined with the Rii value for H in the receptor, in AutoGrid.
#    For example, the Rij_hb for OA-HD H-bonds will be (1.9 + 1.0) Angstrom,
#    and the weighted epsij_hb will be 5.0 kcal/mol * FE_coeff_hbond.
#
#    Atom Rii                         Rij_hb    rec_index
#    Type       epsii       solpar       epsij_hb map_index
#                         vol                      hbond bond_index
#    -- ----------------------------------- --
atom_par H    2.000.020 0.0000 0.000510.00.00-1-13 # Non H-bonding Hydrogen
atom_par HD 2.000.020 0.0000 0.000510.00.02-1-13 # Donor 1 H-bond Hydrogen
atom_par HS 2.000.020 0.0000 0.000510.00.01-1-13 # Donor S Spherical Hydrogen
atom_par C    4.000.15033.5103-0.001430.00.00-1-10 # Non H-bonding Aliphatic Carbon
atom_par A    4.000.15033.5103-0.000520.00.00-1-10 # Non H-bonding Aromatic Carbon
atom_par N    3.500.16022.4493-0.001620.00.00-1-11 # Non H-bonding Nitrogen
atom_par NA 3.500.16022.4493-0.001621.95.04-1-11 # Acceptor 1 H-bond Nitrogen
atom_par NS 3.500.16022.4493-0.001621.95.03-1-11 # Acceptor S Spherical Nitrogen
atom_par OA 3.200.20017.1573-0.002511.95.05-1-12 # Acceptor 2 H-bonds Oxygen
atom_par OS 3.200.20017.1573-0.002511.95.03-1-12 # Acceptor S Spherical Oxygen
atom_par F    3.090.08015.4480-0.001100.00.00-1-14 # Non H-bonding Fluorine
atom_par Mg 1.300.875 1.5600-0.001100.00.00-1-14 # Non H-bonding Magnesium
atom_par MG 1.300.875 1.5600-0.001100.00.00-1-14 # Non H-bonding Magnesium
atom_par P    4.200.20038.7924-0.001100.00.00-1-15 # Non H-bonding Phosphorus
atom_par SA 4.000.20033.5103-0.002142.51.05-1-16 # Acceptor 2 H-bonds Sulphur
atom_par S    4.000.20033.5103-0.002140.00.00-1-16 # Non H-bonding Sulphur
atom_par Cl 4.090.27635.8235-0.001100.00.00-1-14 # Non H-bonding Chlorine
atom_par CL 4.090.27635.8235-0.001100.00.00-1-14 # Non H-bonding Chlorine
atom_par Ca 1.980.550 2.7700-0.001100.00.00-1-14 # Non H-bonding Calcium
atom_par CA 1.980.550 2.7700-0.001100.00.00-1-14 # Non H-bonding Calcium
atom_par Mn 1.300.875 2.1400-0.001100.00.00-1-14 # Non H-bonding Manganese
atom_par MN 1.300.875 2.1400-0.001100.00.00-1-14 # Non H-bonding Manganese
atom_par Fe 1.300.010 1.8400-0.001100.00.00-1-14 # Non H-bonding Iron
atom_par FE 1.300.010 1.8400-0.001100.00.00-1-14 # Non H-bonding Iron
atom_par Zn 1.480.550 1.7000-0.001100.00.00-1-14 # Non H-bonding Zinc
atom_par ZN 1.480.550 1.7000-0.001100.00.00-1-14 # Non H-bonding Zinc
atom_par Br 4.330.38942.5661-0.001100.00.00-1-14 # Non H-bonding Bromine
atom_par BR 4.330.38942.5661-0.001100.00.00-1-14 # Non H-bonding Bromine
atom_par I    4.720.55055.0585-0.001100.00.00-1-14 # Non H-bonding Iodine

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

钟海洋 发表于 2016-4-16 15:10:03

zhouling1019 发表于 2016-1-1 18:33
您好，我想请教一下，我的配体有金原子，我也是按照帖子那麽说的做的，怎麽就不行啊！方面的话，我想加一 ...

请问在具有金属离子的情况下能够正常保存成pdbqt格式吗？我的情况是有的pdb保存成功了，有的却失败了，提示说没有他的力场元素，你有遇到这种情况吗？

钟海洋 发表于 2016-4-16 15:09:39

钟海洋 发表于 2016-4-16 15:09:23

墨竹晓风 发表于 2014-3-5 22:09:03

希望能讲解下参数的含义

shouzhangxin 发表于 2015-1-7 18:05:26

太给力了

shouzhangxin 发表于 2015-1-7 18:06:18

:lol{:soso_e179:}:D:)

夏雷滚滚 发表于 2015-7-21 12:34:14

用了就解决问题了，衷心谢谢

木C鱼 发表于 2015-8-29 10:11:25

为什么没有Cr（铬）的啊，求助！

zhouling1019 发表于 2016-1-1 18:33:34

夏雷滚滚发表于 2015-7-21 12:34
用了就解决问题了，衷心谢谢

您好，我想请教一下，我的配体有金原子，我也是按照帖子那麽说的做的，怎麽就不行啊！方面的话，我想加一下你的qq，可以吗？这个问题已经困扰半月了，真的是太头疼了。

jjw1017 发表于 2016-3-17 14:22:11

通过推荐过来的，看了问题解决了，非常感谢大神的分享。

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Autodock 默认的原子类型及力场添加操作