PDB2ADF:将PDB文件转换为QMMM输入文件

PDB2ADF实用程序是由Marcel Swart编写的。

概述

概述

从ADF2005.01版本开始,官方版本中提供了实用程序PDB2ADF。以前可以在贡献的软件页面上找到此实用程序。 从AMS2020开始,默认值是制作AMSIFIFIED ADF输入,该输入不能与以前的版本一起使用。 如果环境变量SCM_PDB2ADF设置为旧,则可以获得旧样式输入(仅与ADF一起使用<=2019). 如果环境变量SCM_PDB2ADF设置为New(仅与ADF一起使用,则可以获得NewQmmm样式输入输入<=2019).

写入PDB2ADF实用程序以阅读a PDB文件,其中包含蛋白质结构的原子坐标,并将其转化为ADF InputFile,特别是与QMMM计算一起使用。它还可以用于在溶质分子周围设置溶剂壳。

PDB文件通常用于蛋白质结构,并根据某些规则进行格式化,请参阅: http://www.wwpdb.org/docs.html以及下面官方PDB格式的部分。

对于PDB文件中存在的每个残留/分子,应该有一个碎片文件可用,无论是常见的AMS库($ Amshome / atomicData / PDB2ADF目录),还是在调用PDB2ADF程序的本地目录中。本地目录中的片段文件将优先级高于AMS库中的重复级。将片段文件松散地格式化在琥珀色参数文件上,并包含有关残留物的信息;例如,目前的原子,与他们的一般和力域atomnames,原子收费,与其他原子的连接,用于在PDB文件中找不到时的位置;请参阅下面的部分部分文件。 AMS库中可用的是氨基酸残基的片段文件,包括在N-或C-末端残留物中的那些,三种溶剂(水,甲醇,氯仿),一些经常在蛋白质结构(铜,氟)中存在的离子,等等。

还存在于AMS库中的溶剂盒文件,可用于放置围绕蛋白质的溶剂层或溶质。可用的是上述三种溶剂。

读取PDB和相应的片段文件后,程序试图弄清楚缺少哪些原子,并将添加那些原子;它使用片段文件上提供的信息来执行此操作。对于某些氨基酸残基,有几种质子化状态可以是例如质子化状态。组氨酸可以在N-δ位置,在N-δ位置或两者上都是质子化。默认选项是选择天冬氨酸(ASP),谷氨酸(Glu),赖氨酸(Lys)残留物的完全充电选项,并单独决定每个组氨酸(他)和半胱氨酸(Cys)残留物的质子化状态应该是什么。在那些单独的情况下,给出了相邻分子/残基的距离,其可以有助于确定质子化状态。见下面的蛋白质例子。

毕竟设置得当,列表给出了残留名称/数字,您可以从中选择应放在QM系统中的那些;之后,对于每个所选择的QM残差,应该选择选择QM部件的位置。除了处理脯氨酸(Pro)时,截止最合适的点似乎是在C-alpha位置。后一种残留物是环状的,例如,侧网连接到C-alpha Carbon!对于该残余物,可以更好地包括在QM部分中的前述残余物的C-α,H-α和骨架羰基。

该程序将尝试使用“.pdb2adf”替换PDB文件的“.pdb”扩展名为AMS InputFile;为方便起见,该程序还将“.p2a.pdb”文件写入完整的系统,因为程序所做的。然后,如果所有一切都已正确执行,则可以通过传统的查看器程序(例如imol,vmd,molekel,AMSView)来可视化此文件。

下面给出的是两个例子,一个用于施用蛋白质,另一个如何建立溶剂壳运行。

要注意的事情

  • AMS2020中的QMMM实现是新的。它使用AMS混合发动机。
  • 默认情况下,PDB2ADF使AMS混合引擎输入格式。
  • PDB2ADF程序使用琥珀色参数文件,并设置用于与琥珀色强制字段一起使用,版本amber95,该文件是为生物系统而设计的。
  • 有关问题,备注,请联系: 支持@SCM..com.

对于ADF.<=2019 only:

  • 如果环境变量SCM_PDB2ADF设置为Old,则使用旧样式QMMM输入格式。
  • 如果环境变量SCM_PDB2ADF设置为新功能,则使用NewQmmm样式QMMM输入格式。

官方PDB格式

数据类型 场地 定义
1 - 6 记录名称 'atom'或'hetatm'  
7 - 11 整数 序列号 原子序列号。
13 - 16 原子 名称 原子名称。
17 特点 altloc 备用位置指示灯。
18 - 20 残留名称 resname. 残留名称。
22 特点 Chainid. 链标识符。
23 - 26 整数 Resseq. 残留序列号。
27 APHAR. icode. Borderleft插入残留物。
31 - 38 真实(8.3) x 在埃中的x正交坐标。
39 - 46. 真实(8.3) y 在埃中的正交坐标。
47 - 54. 真实(8.3) z 在埃中的z处于正交坐标。
55 - 60 真实(6.2) 占用 占用。
61 - 66. 真实(6.2) Tempfactor. 温度因数。
73 - 76. Lstring(4) SEGID 段标识符,左对齐。
77 - 78. Lstring(2) 元素 元素符号,右对齐。
79 - 80 Lstring(2) 收费 在原子上充电。

来自PDB文件的典型示例:

         1         2         3         4         5         6         7         8
12345678901234567890123456789012345678901234567890123456789012345678901234567890

ATOM     76  O   GLY    A9       6.671  55.354  35.873  1.00 14.75      A
ATOM     77  N   ASN   A10       6.876  53.257  36.629  1.00 16.09      A
ATOM     62  O   GLY A   9       6.791  55.214  35.719  1.00 15.61      4AZU 153
ATOM     63  N   ASN A  10       6.892  53.135  36.555  1.00 12.64      4AZU 154

PDB2ADF实用程序是灵活的,并且应该能够读取大多数PDB文件,甚至是具有不完整或错误的线条格式的文件。从每个attom / hetatm线路,它试图阅读:

  • 原子编号
  • 原子名称
  • Residuename.
  • 链标识符
  • 残留号码
  • x,y,z坐标

提示适当格式化:

  • 始终将属于一个残留物的原子组合在一起
  • 始终在第13-16列上提供原子名称
  • 指定链ID仅使用字母(或空白)

片段文件的内容

下面给出的是水的片段文件的内容。第一行是一个注释行,唯一重要的参数是noconnect关键字,这表明程序不应该尝试与其他残留物/分子进行任何连接。然后遵循三条线,定义残留空间的方向;它们不用于一般碎片,但对于氨基酸残基和DNA核苷酸是相关的并且是重要的。最后,对于分子中的每个原子,在片段中应该有一条线;它的名称要用于PDB文件;琥珀力菲尔德雾化;一个假的雾名;分子中的其他原子的连接和坐标(键,角度,二角角),其可用于给出原子的位置,如果它不存在于PDB文件中;原子充电;声音标记(!)在该片段中与该片段中的其他原子的连接,或者在氨基酸残基/ DNA核苷酸的情况下的其他片段。当前版本尚未使用后​​一个连接,但下一个版本可能会使用它们。

HOH  Water molecule  NOCONNECT
   1   DUMM  DU    M      0   0   0       0.0000      0.0000      0.0000
   2   DUMM  DU    M      1   0   0       1.4490      0.0000      0.0000
   3   DUMM  DU    M      2   1   0       1.5220    111.1000      0.0000
   4   O     OW    O      0   0   0       0.0000      0.0000      0.0000  -0.8340  !  5  6
   5   H1    HW    H      4   0   0       0.9572      0.0000      0.0000   0.4170  !  4
   6   H2    HW    H      4   5   0       0.9572    104.5200      0.0000   0.4170  !  4

溶剂盒文件的内容

第一行是注释行,其次是溶剂盒中的总原子总数的线和盒子的尺寸(在埃中);然后,对于框中的每个原子,原子名称必须与pdb atomname和笛卡尔坐标匹配,并且再次在埃赫斯中。

PDB2ADF的用途

简短的介绍

该计划以交互方式工作,并且应该直接使用。但是,对于输出中的一些阶段,下面给出简短的描述。

                                  P D B 2 A D F - program
                                     version 2008.01
                              Written by: Marcel Swart, 2008

                         This program uses AMBER parameter files
                            see: http://amber.scripps.edu

Do you want a logfile to be written (Y/n) ?

存在此选项以创建PDB2ADF的日志文件。但是,它通常只用于调试目的。

Ignoring atom on line:
ATOM    974   OH LYS A 128     -10.073 42.775 15.690 1.00 38.79     5AZU1065

这是一项警告,即忽略该特定行上的原子,通常仅发生几次(小于十)。还取决于PDB文件遵循PDB格式规则的程度。

Data Processed:
     Nat:       2519
    Nmol:        196
 NChains:          1

有关在PDB文件中读取的信息的信息:原子(NAT)的总数,分子/残基(Nmol)和蛋白质链数(NCHAINS)。

Please wait, making connection tables

此时,通过观察原子距离来制造原子之间的连接。这可能需要一段时间,具体取决于系统的大小。

Do you want to make separate files for each chain (Y/n) ?

您可以选择为不同的蛋白质链制作不同的InputFiles,但您也可以为所有蛋白质链制成一个输入文件。

Found the following terminal amino acid residues : (C-term) 128 (N-term) 1
Do you want to use these as terminal residues (Y/n) ?

关于每个链条的C-和N-末端残留物的信息。据报道,确保正确选择它们。注意,如果C-和N终端残留物连接(可能是可能的情况),请在此处输入n。

Multiple AMBER options for HIS :
  0         Decide every time differently
  1   HID   Histidine Delta Hydrogen
  2   HIE   Histidine Epsilon Hydrogen
  3   HIP   Histidine E & D Hydrogens

Suggested option: 0

对于许多残留物(他的Glu,Asp,Lys和Cys),Amber95力领域中有多个选项,取决于质子化状态(他的Glu,Asp和Lys)或硫桥的存在/连接到金属原子(Cys)。默认值是为他和Cys Resides选择不同的选项,并使用Glu,ASP和LYS的一个选项(完全充电)。但是,如果希望您可以选择所有残留物。

Multiple AMBER options for CYS    3 (    3) :
  1   CYS   Cysteine (SH)
  2   CYM   Deprotonated Cysteine (S-)
  3   CYX   Cystine (S-S bridge)

  Connections and Nearest 原子s for SG CYS    3 SG  ( P2A #   41 PDB#   20 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.82      38      19  CB  CYS    3  CB       1       3.79    2382     980  O   HOH  151  O
 2    2.02     461     193  SG  CYS   26  SG       2       3.80      22       0  HC  GLN    2
                                                   3       4.04    2391     983  O   HOH  154  O
                                                   4       4.15     509     206  O   GLN   28  O
                                                   5       4.18     522       0  HA  PHE   29
Suggestion: 3

给出了Cys3的选项,其中有关与Sg硫原子(左侧)粘合的原子的信息,以及最接近的五个非键合原子(右侧)。这些信息可以帮助您决定为此特定的残留物做出哪种选择。还给出了(底部)是在这种情况下基于硫桥的存在的建议选择。

Multiple AMBER options for HIS   46 (   46) :
  1   HID   Histidine Delta Hydrogen
  2   HIE   Histidine Epsilon Hydrogen
  3   HIP   Histidine E & D Hydrogens

  Connections and Nearest 原子s for ND HIS   46 ND1 ( P2A #  844 PDB#  347 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.37     843     346  CG  HIS   46  CG       1       2.62    2166       0  H1  MET  121
 2    1.33     846     349  CE  HIS   46  CE1      2       3.23    2080     863  ND  HIS  117  ND1
 3    2.04    2318     959  CU  CU   130  CU       3 HB    3.33    2163     900  S   MET  121  SD
                                                   4       3.40    2164     901  CT  MET  121  CE
                                                   5       3.57    2082     865  CE  HIS  117  CE1

  Connections and Nearest 原子s for NE HIS   46 NE2 ( P2A #  848 PDB#  350 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.32     846     349  CE  HIS   46  CE1      1 HB    2.70     162      67  O   ASN   10  O
 2    1.37     850     348  CD  HIS   46  CD2      2       2.83     814       0  H1  MET   44
                                                   3       3.23    2166       0  H1  MET  121
                                                   4       3.52     822     332  O   MET   44  O
                                                   5       3.74     813     334  CT  MET   44  CG
Suggestion: 2

对于他的残留物,给予δ和ε氮原子的信息。还表明(通过HB)是与另外的原子存在氢键。这里使用的定义是,如果它们都是非碳/非氢原子,则两个原子是氢键合,并且它们之间的距离小于原子的范德华半径的距离。这是一个简单的定义,但似乎是有效的。在这种情况下,随着N(DELTA)粘合到铜中,质子应附着在N(epsilon)上。

Making choice for which molecules should be QM, which MM

现在我们来到QM和MM系统中的划分的部分。

Residues belonging to chain  0
Option  Molecule    Option  Molecule    Option  Molecule    Option  Molecule    Option  Molecule
     1: ALA    1        28: GLN   28        55: ASP   55        82: ALA   82       109: ALA  109
     2: GLN    2        29: PHE   29        56: LYS   56        83: HIS   83       110: TYR  110
etc

属于链0的所有分子/残基,具有期权编号。

Give option number of molecules to be put in QM region (or 'c' to continue):
Note: by specifying a negative number a molecule is removed from the QM region

在这里,您将要求您输入要放入QM系统的残差的选项编号。

Putting GLY   45 in QM region
Putting HIS   46 in QM region

在这种情况下,GLY45和HIS46已被放入QM系统中。

Make a choice for the QM/MM treatment of GLY   45
 0:  Put completely in QM region
 1:  Cut off at C-alpha (put NH in QM region, CO in MM region)
 2:  Cut off at C-alpha (put NH in MM region, CO in QM region)
 3:  Cut off at C-alpha (put NH and CO in MM region)
 4:  Cut off at C-alpha (put NH and CO in QM region,  sidechain in MM region)
 5:  Put only part of sidechain in QM region

Suggestion: 2
Give choice:

应选择选择QM系统的位置。通常,这是在C(alpha)位置完成的,并且您应该只选择建议。

Solvent molecules (SOL/HOH) belonging to this chain:
    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20
   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40
   41   42   43   44   45   46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
   61   62   63   64   65   66

Give the number of the molecule to be put in QM region (or 'c' to continue):

水分子也可以放入QM系统中。

Box Shape options:
 1  Spherical box
 2  Cubic box
Make a choice:

要使用的框类型。

Maximum atomic distance (Angs) from center       25.62
Give boxsize (def.:    28.62 Angs)

用于在系统周围放置一层溶剂分子的盒子的大小。最大限度。 dist。是来自蛋白质的质量中心的任何蛋白质原子的最大距离。通常,您应该选择一个尺寸尺寸至少6埃较大的盒子(所以至少两个溶剂分子周围系统)。

Using BOXSIZE value of  30.0000
Adding atoms for box     1  Added (Box):     0 (Total):     0  Excl. (1):   648  Excl. (2):     0
Adding atoms for box     2  Added (Box):     9 (Total):     9  Excl. (1):   639  Excl. (2):     0
Adding atoms for box    63  Added (Box):     3 (Total):  7635  Excl. (1):   645  Excl. (2):     0
Adding atoms for box    64  Added (Box):     0 (Total):  7635  Excl. (1):   648  Excl. (2):     0
Writing inputfile for chain   1

添加了7635个原子(2545个水分子)的总量。

Inputfile(s) written, everything processed, work has been done.
Thank you for using the PDB2ADF program.

================================
Normal ending of PDB2ADF program
================================

已编写ADF InputFile,PDB文件已成为进程。一切都已完成。

蛋白质结构的一个例子

该示例的思想是使用Azurin的PDB进行ADF输入文件(1dyz.pdb.txt.)。该示例的结果应该是在ADF输入文件中,紫红素的活性位点(图1)在QM部分中,其余的蛋白质在MM部分中,并加入溶剂水(在一个盒子),也在mm部分中。

../_images/azurin.png.

图1: 紫红素的活跃点

PDB2ADF的用途

该计划在交互方式工作。在下面给出 大胆的 是用户必须键入的部分。在用户同意该程序给出的建议的情况下,用户可以按下输入的ENTER键 进入.

                                  P D B 2 A D F - program
                                     version 2008.01
                              Written by: Marcel Swart, 2008

                         This program uses AMBER parameter files
                            see: http://amber.scripps.edu

Please give 名称 of PDB-file

1dyz.pdb.txt.

Do you want a logfile to be written (Y/n) ?

进入

 read fragments

Data Processed:
     Nat:       2519
    Nmol:        196
 NChains:          1

Please wait, making connection tables
Now finding nearby atoms
Assigning chain ID to all residues
Completing residues for which only option is available

Found the following terminal amino acid residues : (C-term)   129 (N-term)     1
Do you want to use these as terminal residues (Y/n) ?

进入

Refinding nearby atoms (including atoms added in residue completion)

Multiple AMBER options for HIS :
  0         Decide every time differently
  1   HID   Histidine Delta Hydrogen
  2   HIE   Histidine Epsilon Hydrogen
  3   HIP   Histidine E & D Hydrogens

Suggested option: 0

进入

Using 0: Decide every time differently

Multiple AMBER options for GLU :
  0         Decide every time differently
  1   GLU   Glutamic acid (COO-)
  2   GLH   Neutral Glutamic acid (COOH)

Suggested option: 1

进入

Using 17   GLU   Glutamic acid (COO-)

Multiple AMBER options for ASP :
  0         Decide every time differently
  1   ASP   Aspartic acid (COO-)
  2   ASH   Neutral Aspartatic acid (COOH)

Suggested option: 1

进入

Using 18   ASP   Aspartic acid (COO-)

Multiple AMBER options for LYS :
  0         Decide every time differently
  1   LYS   Charged Lysine (NH3+)
  2   LYN   Neutral Lysine (NH2)

Suggested option: 1

进入

Using 19   LYS   Charged Lysine (NH3+)

Multiple AMBER options for CYS :
  0         Decide every time differently
  1   CYS   Cysteine (SH)
  2   CYM   Deprotonated Cysteine (S-)
  3   CYX   Cystine (S-S bridge)

Suggested option: 0

进入

Using 0: Decide every time differently
 - - - - - - - - - - - - - - - - - - - - - - - - - - -
           Making Choices for Chain      0
 - - - - - - - - - - - - - - - - - - - - - - - - - - -

Multiple AMBER options for CYS    3 (    3) :
  1   CYS   Cysteine (SH)
  2   CYM   Deprotonated Cysteine (S-)
  3   CYX   Cystine (S-S bridge)

  Connections and Nearest 原子s for SG CYS    3 SG  ( P2A #   41 PDB#   20 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.82      38      19  CB  CYS    3  CB       1       3.79    2382     980  O   HOH  151  O
 2    2.02     461     193  SG  CYS   26  SG       2       3.80      22       0  HC  GLN    2
                                                   3       4.04    2391     983  O   HOH  154  O
                                                   4       4.15     509     206  O   GLN   28  O
                                                   5       4.18     522       0  HA  PHE   29
Suggestion: 3

进入

Multiple AMBER options for CYS   26 (   26) :
  1   CYS   Cysteine (SH)
  2   CYM   Deprotonated Cysteine (S-)
  3   CYX   Cystine (S-S bridge)

  Connections and Nearest 原子s for SG CYS   26 SG  ( P2A #  461 PDB#  193 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.82     458     192  CB  CYS   26  CB       1       3.41     522       0  HA  PHE   29
 2    2.02      41      20  SG  CYS    3  SG       2       3.43     411     168  O   ASP   23  O
                                                   3       3.60    2322     960  O   HOH  131  O
                                                   4       3.91     403     169  CB  ASP   23  CB
                                                   5       4.15     387       0  HC  VAL   22
Suggestion: 3

进入

Multiple AMBER options for HIS   32 (   32) :
  1   HID   Histidine Delta Hydrogen
  2   HIE   Histidine Epsilon Hydrogen
  3   HIP   Histidine E & D Hydrogens

  Connections and Nearest 原子s for ND HIS   32 ND1 ( P2A #  581 PDB#  244 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.39     580     243  CG  HIS   32  CG       1       3.41     545       0  HC  THR   30
 2    1.33     583     246  CE  HIS   32  CE1      2       3.43      76      33  O   ALA    5  O
                                                   3       3.58      90      40  OH  THR    6  OG1
                                                   4       3.99      91       0  HO  THR    6
                                                   5       4.17      68       0  H   ALA    5

  Connections and Nearest 原子s for NE HIS   32 NE2 ( P2A #  585 PDB#  247 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.31     583     246  CE  HIS   32  CE1      1       2.86     544       0  HC  THR   30
 2    1.37     587     245  CD  HIS   32  CD2      2       3.00     545       0  HC  THR   30
                                                   3       3.14    1677       0  HO  SER   94
                                                   4       3.42     542     229  CT  THR   30  CG2
                                                   5       3.65    1676     688  OH  SER   94  OG
Suggestion: 1

3

Multiple AMBER options for HIS   35 (   35) :
  1   HID   Histidine Delta Hydrogen
  2   HIE   Histidine Epsilon Hydrogen
  3   HIP   Histidine E & D Hydrogens

  Connections and Nearest 原子s for ND HIS   35 ND1 ( P2A #  649 PDB#  271 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.38     648     270  CG  HIS   35  CG       1       2.46     682       0  H   GLY   37
 2    1.32     651     273  CE  HIS   35  CE1      2       2.69    1604       0  H1  GLY   89
                                                   3       3.31     681     282  N   GLY   37  N
                                                   4       3.56    1602     653  CT  GLY   89  CA
                                                   5       3.67     152       0  H1  ASN   10

  Connections and Nearest 原子s for NE HIS   35 NE2 ( P2A #  653 PDB#  274 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.33     651     273  CE  HIS   35  CE1      1 HB    2.91     822     332  O   MET   44  O
 2    1.37     655     272  CD  HIS   35  CD2      2       3.24     814       0  H1  MET   44
                                                   3       3.24     850     348  CD  HIS   46  CD2
                                                   4       3.34    1593       0  H1  GLY   88
                                                   5       3.75     848     350  NE  HIS   46  NE2
Suggestion: 2

3

Multiple AMBER options for HIS   46 (   46) :
  1   HID   Histidine Delta Hydrogen
  2   HIE   Histidine Epsilon Hydrogen
  3   HIP   Histidine E & D Hydrogens

  Connections and Nearest 原子s for ND HIS   46 ND1 ( P2A #  844 PDB#  347 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.37     843     346  CG  HIS   46  CG       1       2.62    2166       0  H1  MET  121
 2    1.33     846     349  CE  HIS   46  CE1      2       3.23    2080     863  ND  HIS  117  ND1
 3    2.04    2318     959  CU  CU   130  CU       3 HB    3.33    2163     900  S   MET  121  SD
                                                   4       3.40    2164     901  CT  MET  121  CE
                                                   5       3.57    2082     865  CE  HIS  117  CE1

  Connections and Nearest 原子s for NE HIS   46 NE2 ( P2A #  848 PDB#  350 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.32     846     349  CE  HIS   46  CE1      1 HB    2.70     162      67  O   ASN   10  O
 2    1.37     850     348  CD  HIS   46  CD2      2       2.83     814       0  H1  MET   44
                                                   3       3.23    2166       0  H1  MET  121
                                                   4       3.52     822     332  O   MET   44  O
                                                   5       3.74     813     334  CT  MET   44  CG
Suggestion: 2

进入

Multiple AMBER options for HIS   83 (   83) :
  1   HID   Histidine Delta Hydrogen
  2   HIE   Histidine Epsilon Hydrogen
  3   HIP   Histidine E & D Hydrogens

  Connections and Nearest 原子s for ND HIS   83 ND1 ( P2A # 1494 PDB#  613 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.39    1493     612  CG  HIS   83  CG       1       2.67    1317       0  HC  VAL   73
 2    1.33    1496     615  CE  HIS   83  CE1      2       3.63    1315     542  CT  VAL   73  CG2
                                                   3       3.74    1310       0  HC  VAL   73
                                                   4       3.82    1316       0  HC  VAL   73
                                                   5       3.86    1313       0  HC  VAL   73

  Connections and Nearest 原子s for NE HIS   83 NE2 ( P2A # 1498 PDB#  616 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.32    1496     615  CE  HIS   83  CE1      1       3.09    1313       0  HC  VAL   73
 2    1.38    1500     614  CD  HIS   83  CD2      2       3.44    1317       0  HC  VAL   73
                                                   3       3.88    2385     981  O   HOH  152  O
                                                   4       3.93    1311     541  CT  VAL   73  CG1
                                                   5       4.03    1309     540  CT  VAL   73  CB
Suggestion: 2

3

Multiple AMBER options for CYS  112 (  112) :
  1   CYS   Cysteine (SH)
  2   CYM   Deprotonated Cysteine (S-)
  3   CYX   Cystine (S-S bridge)

  Connections and Nearest 原子s for SG CYS  112 SG  ( P2A # 2001 PDB#  828 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.82    1998     827  CB  CYS  112  CB       1       2.53     858       0  H   ASN   47
 2    2.14    2318     959  CU  CU   130  CU       2       2.65    2023       0  H   PHE  114
                                                   3       3.00    2028       0  HC  PHE  114
                                                   4       3.29     868       0  H   ASN   47
                                                   5       3.39    2027       0  HC  PHE  114
Suggestion: 2

进入

Multiple AMBER options for HIS  117 (  117) :
  1   HID   Histidine Delta Hydrogen
  2   HIE   Histidine Epsilon Hydrogen
  3   HIP   Histidine E & D Hydrogens

  Connections and Nearest 原子s for ND HIS  117 ND1 ( P2A # 2080 PDB#  863 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.37    2079     862  CG  HIS  117  CG       1       2.82    2028       0  HC  PHE  114
 2    1.34    2082     865  CE  HIS  117  CE1      2       3.23     844     347  ND  HIS   46  ND1
 3    1.99    2318     959  CU  CU   130  CU       3       3.26    2031       0  HA  PHE  114
                                                   4       3.27     832     340  O   GLY   45  O
                                                   5       3.43     846     349  CE  HIS   46  CE1

  Connections and Nearest 原子s for NE HIS  117 NE2 ( P2A # 2084 PDB#  866 )
      Dist  P2A Nr  PDB Nr  Label                 Near     Dist  P2A Nr  PDB Nr  Label
 1    1.31    2082     865  CE  HIS  117  CE1      1       2.57     209       0  H1  MET   13
 2    1.37    2086     864  CD  HIS  117  CD2      2       2.65    2031       0  HA  PHE  114
                                                   3 HB    2.74    2406     988  O   HOH  159  O
                                                   4       3.34    2030     841  CA  PHE  114  CD1
                                                   5       3.41     204       0  H1  MET   13
Suggestion: 2

进入

 - - - - - - - - - - - - - - - - - - - - - - - - - - -
           Making Choices for Chain      1
 - - - - - - - - - - - - - - - - - - - - - - - - - - -

Completing residues with multiple options available, and solvent molecules

Checking positions of newly added atoms

Making choice for which molecules should be QM, which MM

Residues belonging to chain  0
Option  Molecule    Option  Molecule    Option  Molecule    Option  Molecule    Option  Molecule
     1: ALA    1        28: GLN   28        55: ASP   55        82: ALA   82       109: ALA  109
     2: GLN    2        29: PHE   29        56: LYS   56        83: HIS   83       110: TYR  110
     3: CYS    3        30: THR   30        57: GLN   57        84: THR   84       111: PHE  111
     4: GLU    4        31: MET   31        58: ALA   58        85: LYS   85       112: CYS  112
     5: ALA    5        32: HIS   32        59: VAL   59        86: VAL   86       113: SER  113
     6: THR    6        33: LEU   33        60: ALA   60        87: ILE   87       114: PHE  114
     7: VAL    7        34: LYS   34        61: THR   61        88: GLY   88       115: PRO  115
     8: GLU    8        35: HIS   35        62: ASP   62        89: GLY   89       116: GLY  116
     9: SER    9        36: VAL   36        63: GLY   63        90: GLY   90       117: HIS  117
    10: ASN   10        37: GLY   37        64: MET   64        91: GLU   91       118: TRP  118
    11: ASP   11        38: LYS   38        65: GLY   65        92: SER   92       119: ALA  119
    12: ALA   12        39: MET   39        66: ALA   66        93: ASP   93       120: MET  120
    13: MET   13        40: ALA   40        67: GLY   67        94: SER   94       121: MET  121
    14: GLN   14        41: LYS   41        68: LEU   68        95: VAL   95       122: LYS  122
    15: TYR   15        42: VAL   42        69: ALA   69        96: THR   96       123: GLY  123
    16: ASN   16        43: ALA   43        70: GLN   70        97: PHE   97       124: THR  124
    17: VAL   17        44: MET   44        71: ASP   71        98: ASP   98       125: LEU  125
    18: LYS   18        45: GLY   45        72: TYR   72        99: VAL   99       126: LYS  126
    19: GLU   19        46: HIS   46        73: VAL   73       100: SER  100       127: LEU  127
    20: ILE   20        47: ASN   47        74: LYS   74       101: LYS  101       128: GLY  128
    21: VAL   21        48: LEU   48        75: ALA   75       102: ILE  102       129: SER  129
    22: VAL   22        49: VAL   49        76: GLY   76       103: ALA  103       130: CU   130
    23: ASP   23        50: LEU   50        77: ASP   77       104: ALA  104
    24: LYS   24        51: THR   51        78: THR   78       105: GLY  105
    25: SER   25        52: LYS   52        79: ARG   79       106: GLU  106
    26: CYS   26        53: ASP   53        80: VAL   80       107: ASN  107
    27: LYS   27        54: ALA   54        81: ILE   81       108: TYR  108

Give option number of molecules to be put in QM region (or 'c' to continue):
Note: by specifying a negative number a molecule is removed from the QM region

45 46 112 117 121 130

Putting GLY   45 in QM region
Putting HIS   46 in QM region
Putting CYS  112 in QM region
Putting HIS  117 in QM region
Putting MET  121 in QM region
Putting CU   130 in QM region

Give option number of molecules to be put in QM region (or 'c' to continue):
Note: by specifying a negative number a molecule is removed from the QM region

c

Make a choice for the QM/MM treatment of GLY   45
 0:  Put completely in QM region
 1:  Cut off at C-alpha (put NH in QM region, CO in MM region)
 2:  Cut off at C-alpha (put NH in MM region, CO in QM region)
 3:  Cut off at C-alpha (put NH and CO in MM region)
 4:  Cut off at C-alpha (put NH and CO in QM region,  sidechain in MM region)
 5:  Put only part of sidechain in QM region

Suggestion: 2
Give choice:

进入

Make a choice for the QM/MM treatment of HIS   46
 0:  Put completely in QM region
 1:  Cut off at C-alpha (put NH in QM region, CO in MM region)
 2:  Cut off at C-alpha (put NH in MM region, CO in QM region)
 3:  Cut off at C-alpha (put NH and CO in MM region)
 4:  Cut off at C-alpha (put NH and CO in QM region,  sidechain in MM region)
 5:  Put only part of sidechain in QM region

Suggestion: 1
Give choice:

进入

Make a choice for the QM/MM treatment of CYS  112
 0:  Put completely in QM region
 1:  Cut off at C-alpha (put NH in QM region, CO in MM region)
 2:  Cut off at C-alpha (put NH in MM region, CO in QM region)
 3:  Cut off at C-alpha (put NH and CO in MM region)
 4:  Cut off at C-alpha (put NH and CO in QM region,  sidechain in MM region)
 5:  Put only part of sidechain in QM region

Suggestion: 3
Give choice:

进入

Make a choice for the QM/MM treatment of HIS  117
 0:  Put completely in QM region
 1:  Cut off at C-alpha (put NH in QM region, CO in MM region)
 2:  Cut off at C-alpha (put NH in MM region, CO in QM region)
 3:  Cut off at C-alpha (put NH and CO in MM region)
 4:  Cut off at C-alpha (put NH and CO in QM region,  sidechain in MM region)
 5:  Put only part of sidechain in QM region

Suggestion: 3
Give choice:

进入

Make a choice for the QM/MM treatment of MET  121
 0:  Put completely in QM region
 1:  Cut off at C-alpha (put NH in QM region, CO in MM region)
 2:  Cut off at C-alpha (put NH in MM region, CO in QM region)
 3:  Cut off at C-alpha (put NH and CO in MM region)
 4:  Cut off at C-alpha (put NH and CO in QM region,  sidechain in MM region)
 5:  Put only part of sidechain in QM region

Suggestion: 3
Give choice:

进入

Make a choice for the QM/MM treatment of CU   130
 0:  Put completely in QM region
 1:  Put only part of molecule in QM region

Suggestion: 0
Give choice:

进入

Total formal 收费 on molecule CU    130      2.0000

Solvent molecules (SOL/HOH) belonging to this chain:
    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20
   21   22   23   24   25   26   27   28   29   30   31   32   33   34   35   36   37   38   39   40
   41   42   43   44   45   46   47   48   49   50   51   52   53   54   55   56   57   58   59   60
   61   62   63   64   65   66

Give the number of the molecule to be put in QM region (or 'c' to continue):

c

Residues belonging to chain  1

Do you want to add solvent to your system (Y/n) ?

进入

Solvent (box) available:
   1:  HOH     HOH  Water molecule
   2:  MOH     MOH  Methanol molecule
   3:  CHL     CHL  Chloroform molecule

1

Reading contents of solvent box p2abox.HOH

Box Shape options:
 1  Spherical box
 2  Cubic box
Make a choice:

1

Writing inputfile for chain   0

Using total 收费   1.0 and total spin   1.0

Maximum atomic distance (Angs) from center       25.62
Give boxsize (def.:    28.62 Angs)

30.0

Using BOXSIZE value of  30.0000
Adding atoms for box     1  Added (Box):     0 (Total):     0  Excl. (1):   648  Excl. (2):     0
Adding atoms for box     2  Added (Box):     9 (Total):     9  Excl. (1):   639  Excl. (2):     0
Adding atoms for box     3  Added (Box):     3 (Total):    12  Excl. (1):   645  Excl. (2):     0
Adding atoms for box     4  Added (Box):     0 (Total):    12  Excl. (1):   648  Excl. (2):     0
Adding atoms for box     5  Added (Box):     6 (Total):    18  Excl. (1):   642  Excl. (2):     0
Adding atoms for box     6  Added (Box):   228 (Total):   246  Excl. (1):   420  Excl. (2):     0
Adding atoms for box     7  Added (Box):   219 (Total):   465  Excl. (1):   429  Excl. (2):     0
Adding atoms for box     8  Added (Box):     9 (Total):   474  Excl. (1):   639  Excl. (2):     0
Adding atoms for box     9  Added (Box):     0 (Total):   474  Excl. (1):   648  Excl. (2):     0
Adding atoms for box    10  Added (Box):   225 (Total):   699  Excl. (1):   423  Excl. (2):     0
Adding atoms for box    11  Added (Box):   216 (Total):   915  Excl. (1):   432  Excl. (2):     0
Adding atoms for box    12  Added (Box):     6 (Total):   921  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    13  Added (Box):     0 (Total):   921  Excl. (1):   648  Excl. (2):     0
Adding atoms for box    14  Added (Box):     6 (Total):   927  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    15  Added (Box):    12 (Total):   939  Excl. (1):   636  Excl. (2):     0
Adding atoms for box    16  Added (Box):     0 (Total):   939  Excl. (1):   648  Excl. (2):     0
Adding atoms for box    17  Added (Box):    12 (Total):   951  Excl. (1):   636  Excl. (2):     0
Adding atoms for box    18  Added (Box):   210 (Total):  1161  Excl. (1):   438  Excl. (2):     0
Adding atoms for box    19  Added (Box):   219 (Total):  1380  Excl. (1):   429  Excl. (2):     0
Adding atoms for box    20  Added (Box):     3 (Total):  1383  Excl. (1):   645  Excl. (2):     0
Adding atoms for box    21  Added (Box):   216 (Total):  1599  Excl. (1):   417  Excl. (2):    15
Adding atoms for box    22  Added (Box):   381 (Total):  1980  Excl. (1):     3  Excl. (2):   264
Adding atoms for box    23  Added (Box):   261 (Total):  2241  Excl. (1):     3  Excl. (2):   384
Adding atoms for box    24  Added (Box):   183 (Total):  2424  Excl. (1):   423  Excl. (2):    42
Adding atoms for box    25  Added (Box):   189 (Total):  2613  Excl. (1):   426  Excl. (2):    33
Adding atoms for box    26  Added (Box):   186 (Total):  2799  Excl. (1):     3  Excl. (2):   459
Adding atoms for box    27  Added (Box):   351 (Total):  3150  Excl. (1):     3  Excl. (2):   294
Adding atoms for box    28  Added (Box):   222 (Total):  3372  Excl. (1):   420  Excl. (2):     6
Adding atoms for box    29  Added (Box):     9 (Total):  3381  Excl. (1):   639  Excl. (2):     0
Adding atoms for box    30  Added (Box):   162 (Total):  3543  Excl. (1):   429  Excl. (2):    57
Adding atoms for box    31  Added (Box):   219 (Total):  3762  Excl. (1):   426  Excl. (2):     3
Adding atoms for box    32  Added (Box):     6 (Total):  3768  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    33  Added (Box):     6 (Total):  3774  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    34  Added (Box):   219 (Total):  3993  Excl. (1):   426  Excl. (2):     3
Adding atoms for box    35  Added (Box):   216 (Total):  4209  Excl. (1):   432  Excl. (2):     0
Adding atoms for box    36  Added (Box):     6 (Total):  4215  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    37  Added (Box):   219 (Total):  4434  Excl. (1):   426  Excl. (2):     3
Adding atoms for box    38  Added (Box):   279 (Total):  4713  Excl. (1):     6  Excl. (2):   363
Adding atoms for box    39  Added (Box):   231 (Total):  4944  Excl. (1):     0  Excl. (2):   417
Adding atoms for box    40  Added (Box):   195 (Total):  5139  Excl. (1):   432  Excl. (2):    21
Adding atoms for box    41  Added (Box):   231 (Total):  5370  Excl. (1):   414  Excl. (2):     3
Adding atoms for box    42  Added (Box):   324 (Total):  5694  Excl. (1):     0  Excl. (2):   324
Adding atoms for box    43  Added (Box):   408 (Total):  6102  Excl. (1):     6  Excl. (2):   234
Adding atoms for box    44  Added (Box):   204 (Total):  6306  Excl. (1):   435  Excl. (2):     9
Adding atoms for box    45  Added (Box):     6 (Total):  6312  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    46  Added (Box):   177 (Total):  6489  Excl. (1):   435  Excl. (2):    36
Adding atoms for box    47  Added (Box):   219 (Total):  6708  Excl. (1):   429  Excl. (2):     0
Adding atoms for box    48  Added (Box):     6 (Total):  6714  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    49  Added (Box):     0 (Total):  6714  Excl. (1):   648  Excl. (2):     0
Adding atoms for box    50  Added (Box):     3 (Total):  6717  Excl. (1):   645  Excl. (2):     0
Adding atoms for box    51  Added (Box):     6 (Total):  6723  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    52  Added (Box):     0 (Total):  6723  Excl. (1):   648  Excl. (2):     0
Adding atoms for box    53  Added (Box):     9 (Total):  6732  Excl. (1):   639  Excl. (2):     0
Adding atoms for box    54  Added (Box):   222 (Total):  6954  Excl. (1):   426  Excl. (2):     0
Adding atoms for box    55  Added (Box):   213 (Total):  7167  Excl. (1):   426  Excl. (2):     9
Adding atoms for box    56  Added (Box):     6 (Total):  7173  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    57  Added (Box):     3 (Total):  7176  Excl. (1):   645  Excl. (2):     0
Adding atoms for box    58  Added (Box):   219 (Total):  7395  Excl. (1):   423  Excl. (2):     6
Adding atoms for box    59  Added (Box):   219 (Total):  7614  Excl. (1):   429  Excl. (2):     0
Adding atoms for box    60  Added (Box):     6 (Total):  7620  Excl. (1):   642  Excl. (2):     0
Adding atoms for box    61  Added (Box):     0 (Total):  7620  Excl. (1):   648  Excl. (2):     0
Adding atoms for box    62  Added (Box):    12 (Total):  7632  Excl. (1):   636  Excl. (2):     0
Adding atoms for box    63  Added (Box):     3 (Total):  7635  Excl. (1):   645  Excl. (2):     0
Adding atoms for box    64  Added (Box):     0 (Total):  7635  Excl. (1):   648  Excl. (2):     0

Total spin   1.0

Writing inputfile for chain   1
There are no atoms in this chain, ignoring it

Inputfile(s) written, everything processed, work has been done.
Thank you for using the PDB2ADF program.

================================
Normal ending of PDB2ADF program
================================

PDB2ADF生成的1dyz.pdb2adf文件的内容

该文件未完全给出,因为它包含超过9000个原子。

#! /bin/sh

$AMSBIN/ams << eor
System
  Charge   1.0
  Atoms
    N     -1.1930    25.6890    17.1840 region=MM ForceField.Charge=.141400    ForceField.Type=N3   !     1 ALA      1 N   
    H     -0.3133    25.1929    17.1970 region=MM ForceField.Charge=.199700    ForceField.Type=H    !     2 ALA      1 H1  
    H     -1.3738    25.1438    18.0148 region=MM ForceField.Charge=.199700    ForceField.Type=H    !     3 ALA      1 H2  
    H     -1.5170    24.8559    16.7138 region=MM ForceField.Charge=.199700    ForceField.Type=H    !     4 ALA      1 H3  
    C     -1.4820    27.1340    16.8960 region=MM ForceField.Charge=.096200    ForceField.Type=CT   !     5 ALA      1 CA  
    H     -2.1350    27.2082    16.0264 region=MM ForceField.Charge=.088900    ForceField.Type=HP   !     6 ALA      1 HA  
    C     -2.1950    27.7860    18.0880 region=MM ForceField.Charge=-.059700   ForceField.Type=CT   !     7 ALA      1 CB  
    H     -1.5602    27.7210    18.9717 region=MM ForceField.Charge=.030000    ForceField.Type=HC   !     8 ALA      1 HB1 
    H     -2.3971    28.8331    17.8627 region=MM ForceField.Charge=.030000    ForceField.Type=HC   !     9 ALA      1 HB2 
    H     -3.1350    27.2677    18.2776 region=MM ForceField.Charge=.030000    ForceField.Type=HC   !    10 ALA      1 HB3 
    C     -0.1820    27.8790    16.5880 region=MM ForceField.Charge=.616300    ForceField.Type=C    !    11 ALA      1 C   
    O      0.8890    27.4920    17.0690 region=MM ForceField.Charge=-.572200   ForceField.Type=O    !    12 ALA      1 O   
    N     -0.2890    28.9420    15.7940 region=MM ForceField.Charge=-.415700   ForceField.Type=N    !    13 GLN      2 N   
    ...
    H     11.6901     6.5638    30.5231 region=MM ForceField.Charge=.271900    ForceField.Type=H    !   690 GLY     45 H   
    C     11.3760     8.5410    29.7530 region=QM ForceField.Charge=-.025200   ForceField.Type=CT   !   691 GLY     45 CA  
    H     10.9114     9.3322    30.3413 region=QM ForceField.Charge=.069800    ForceField.Type=H1   !   692 GLY     45 HA2 
    H     12.4602     8.6423    29.8009 region=QM ForceField.Charge=.069800    ForceField.Type=H1   !   693 GLY     45 HA3 
    C     10.9630     8.7450    28.3090 region=QM ForceField.Charge=.597300    ForceField.Type=C    !   694 GLY     45 C   
    O     10.8510     7.7910    27.5300 region=QM ForceField.Charge=-.567900   ForceField.Type=O    !   695 GLY     45 O   
    N     10.6890     9.9800    27.9260 region=QM ForceField.Charge=-.415700   ForceField.Type=N    !   696 HIS     46 N   
    H     10.7572    10.7382    28.5898 region=QM ForceField.Charge=.271900    ForceField.Type=H    !   697 HIS     46 H   
    C     10.2900    10.2500    26.5530 region=QM ForceField.Charge=-.058100   ForceField.Type=CT   !   698 HIS     46 CA  
    H     10.5517     9.3991    25.9240 region=QM ForceField.Charge=.136000    ForceField.Type=H1   !   699 HIS     46 HA  
    C      8.7770    10.5120    26.4440 region=QM ForceField.Charge=-.007400   ForceField.Type=CT   !   700 HIS     46 CB  
    H      8.5050    11.3473    27.0893 region=QM ForceField.Charge=.036700    ForceField.Type=HC   !   701 HIS     46 HB2 
    H      8.5229    10.7532    25.4118 region=QM ForceField.Charge=.036700    ForceField.Type=HC   !   702 HIS     46 HB3 
    C      7.9110     9.3590    26.8430 region=QM ForceField.Charge=.186800    ForceField.Type=CC   !   703 HIS     46 CG  
    N      8.0710     8.0910    26.3490 region=QM ForceField.Charge=-.543200   ForceField.Type=NB   !   704 HIS     46 ND1 
    C      7.1230     7.3010    26.8370 region=QM ForceField.Charge=.163500    ForceField.Type=CR   !   705 HIS     46 CE1 
    H      7.0894     6.2496    26.5516 region=QM ForceField.Charge=.143500    ForceField.Type=H5   !   706 HIS     46 HE1 
    N      6.3580     8.0230    27.6330 region=QM ForceField.Charge=-.279500   ForceField.Type=NA   !   707 HIS     46 NE2 
    H      5.5568     7.6742    28.1395 region=QM ForceField.Charge=.333900    ForceField.Type=H    !   708 HIS     46 HE2 
    C      6.8210     9.3110    27.6620 region=QM ForceField.Charge=-.220700   ForceField.Type=CW   !   709 HIS     46 CD2 
    H      6.3141    10.0588    28.2719 region=QM ForceField.Charge=.186200    ForceField.Type=H4   !   710 HIS     46 HD2 
    C     10.9790    11.4950    26.0450 region=MM ForceField.Charge=.597300    ForceField.Type=C    !   711 HIS     46 C   
    ...
    C     11.0290     8.8020    20.9600 region=QM ForceField.Charge=.035000    ForceField.Type=CT   !  1648 CYS    112 CA  
    H     11.3902     9.8061    21.1823 region=QM ForceField.Charge=.048000    ForceField.Type=H1   !  1649 CYS    112 HA  
    C     10.0620     8.3640    22.0630 region=QM ForceField.Charge=-.736000   ForceField.Type=CT   !  1650 CYS    112 CB  
    H      9.2477     9.0845    22.1402 region=QM ForceField.Charge=.244000    ForceField.Type=H1   !  1651 CYS    112 HB3 
    H      9.6557     7.3817    21.8218 region=QM ForceField.Charge=.244000    ForceField.Type=H1   !  1652 CYS    112 HB2 
    S     10.8340     8.2410    23.7100 region=QM ForceField.Charge=-.736000   ForceField.Type=SH   !  1653 CYS    112 SG  
    C     10.1650     3.3080    22.4340 region=QM ForceField.Charge=-.058100   ForceField.Type=CT   !  1710 HIS    117 CA  
    H      9.2929     2.7403    22.7584 region=QM ForceField.Charge=.136000    ForceField.Type=H1   !  1711 HIS    117 HA  
    C     10.1750     4.6030    23.2620 region=QM ForceField.Charge=-.007400   ForceField.Type=CT   !  1712 HIS    117 CB  
    H     11.1220     5.1220    23.1143 region=QM ForceField.Charge=.036700    ForceField.Type=HC   !  1713 HIS    117 HB2 
    H      9.3551     5.2459    22.9418 region=QM ForceField.Charge=.036700    ForceField.Type=HC   !  1714 HIS    117 HB3 
    C     10.0160     4.3980    24.7440 region=QM ForceField.Charge=.186800    ForceField.Type=CC   !  1715 HIS    117 CG  
    N      9.7040     5.4090    25.6080 region=QM ForceField.Charge=-.543200   ForceField.Type=NB   !  1716 HIS    117 ND1 
    C      9.6570     4.9300    26.8540 region=QM ForceField.Charge=.163500    ForceField.Type=CR   !  1717 HIS    117 CE1 
    H      9.4228     5.5952    27.6851 region=QM ForceField.Charge=.143500    ForceField.Type=H5   !  1718 HIS    117 HE1 
    N      9.9280     3.6450    26.8000 region=QM ForceField.Charge=-.279500   ForceField.Type=NA   !  1719 HIS    117 NE2 
    H      9.9617     3.0260    27.5974 region=QM ForceField.Charge=.333900    ForceField.Type=H    !  1720 HIS    117 HE2 
    C     10.1580     3.2710    25.4990 region=QM ForceField.Charge=-.220700   ForceField.Type=CW   !  1721 HIS    117 CD2 
    H     10.3982     2.2340    25.2644 region=QM ForceField.Charge=.186200    ForceField.Type=H4   !  1722 HIS    117 HD2 
    C      6.0350     6.2800    19.5280 region=QM ForceField.Charge=-.023700   ForceField.Type=CT   !  1778 MET    121 CA  
    H      4.9702     6.5113    19.5559 region=QM ForceField.Charge=.088000    ForceField.Type=H1   !  1779 MET    121 HA  
    C      6.6730     6.7710    20.8330 region=QM ForceField.Charge=.034200    ForceField.Type=CT   !  1780 MET    121 CB  
    H      7.7511     6.6157    20.7919 region=QM ForceField.Charge=.024100    ForceField.Type=HC   !  1781 MET    121 HB2 
    H      6.4641     7.8329    20.9631 region=QM ForceField.Charge=.024100    ForceField.Type=HC   !  1782 MET    121 HB3 
    C      6.1560     6.0500    22.0720 region=QM ForceField.Charge=.001800    ForceField.Type=CT   !  1783 MET    121 CG  
    H      5.0693     6.1257    22.1101 region=QM ForceField.Charge=.044000    ForceField.Type=H1   !  1784 MET    121 HG2 
    H      6.4453     5.0000    22.0292 region=QM ForceField.Charge=.044000    ForceField.Type=H1   !  1785 MET    121 HG3 
    S      6.7760     6.6970    23.6140 region=QM ForceField.Charge=-.273700   ForceField.Type=S    !  1786 MET    121 SD  
    C      6.0690     8.3070    23.6050 region=QM ForceField.Charge=-.053600   ForceField.Type=CT   !  1787 MET    121 CE  
    H      4.9825     8.2271    23.5709 region=QM ForceField.Charge=.068400    ForceField.Type=H1   !  1788 MET    121 HE1 
    H      6.3654     8.8396    24.5086 region=QM ForceField.Charge=.068400    ForceField.Type=H1   !  1789 MET    121 HE2 
    H      6.4202     8.8537    22.7299 region=QM ForceField.Charge=.068400    ForceField.Type=H1   !  1790 MET    121 HE3 
    CU     9.5640     7.3450    25.1750 region=QM ForceField.Charge=2.000000   ForceField.Type=CU   !  1915 CU     130 CU  
    ...
    O     31.1328    34.4612    22.6903 region=MM ForceField.Charge=-.834000   ForceField.Type=OW   !  9746 HOH  2545 O   
    H     31.8908    34.5740    22.1167 region=MM ForceField.Charge=.417000    ForceField.Type=HW   !  9747 HOH  2545 H1  
    H     30.6706    35.2981    22.6446 region=MM ForceField.Charge=.417000    ForceField.Type=HW   !  9748 HOH  2545 H2  
  End

  BondOrders
        1      5 1.0
        1      2 1.0
        1      3 1.0
        1      4 1.0
        5      7 1.0
        5     11 1.0
        5      6 1.0
        7      8 1.0
        7      9 1.0
        7     10 1.0
       11     12 1.0
       11     13 1.0
       13     15 1.0
       13     14 1.0
       15     17 1.0
       15     28 1.0
       15     16 1.0
       17     20 1.0
       17     18 1.0
       17     19 1.0
     ...
     9746   9747 1.0
     9746   9748 1.0
  End
End

Task GeometryOptimization

GeometryOptimization
  MaxIterations 100
  Convergence Gradients=1e-3
End
Engine Hybrid
  QMMM QMRegion=QM QMEngineID=ADF MMEngineID=ForceField

  Capping
    AtomicInfoForCappingAtom ForceField.Type=H1 ForceField.Charge=0.0
  End
  Engine ADF
    Title QM/MM calculation setup by pdb2adf: M.Swart et al., 2020
    Symmetry NOSYM

    Eprint
      SFO NOEIG NOOVL
    End

    XC
      GGA BP86
    End

    Basis
      type TZP
      core small
    End

    SCF
      diis ok=0.01
      Converge 1.0e-5 1.0e-5
      Iterations 99
    End
    Unrestricted
    SpinPolarization   1.0
  EndEngine
  Engine ForceField
    Type Amber95
    ForceFieldFile $AMSHOME/atomicdata/ForceFields/amber95.ff
  EndEngine
EndEngine
eor

溶剂壳运行的一个例子

这个例子的想法是使用PDB文件进行ADF输入文件(hoh.pdb.txt.),在溶剂甲醇中。 ADF输入文件中的水分子应在QM部分中,溶剂甲醇(在盒子中)是MM部分。

HOH.PDB文件的内容

TITLE     PDB-FILE CORRESPONDING TO pdb2adf-GENERATED adf.-INPUTFILE
REMARK    Written by M. Swart, March 2005
HETATM    1 H1   HOH     1       1.716  26.282  11.239  1.00  0.00      1DYZ H
HETATM    2 O    HOH     1       2.439  25.795  11.634  1.00  0.00      1DYZ O
HETATM    3 H2   HOH     1       3.140  26.440  11.729  1.00  0.00      1DYZ H
END   

PDB2ADF的用途

该计划在交互方式工作。在下面给出 大胆的 是用户必须键入的部分。在用户同意该程序给出的建议的情况下,用户可以按下输入的ENTER键 进入.

                                  P D B 2 A D F - program
                                     version 2008.01
                              Written by: Marcel Swart, 2008

                         This program uses AMBER parameter files
                            see: http://amber.scripps.edu
Please give 名称 of PDB-file

hoh.pdb.txt.

Do you want a logfile to be written (Y/n) ?

进入

 read fragments

Data Processed:
     Nat:          3
    Nmol:          1
 NChains:          0

Please wait, making connection tables
Now finding nearby atoms
Assigning chain ID to all residues
Completing residues for which only option is available

Refinding nearby atoms (including atoms added in residue completion)

 - - - - - - - - - - - - - - - - - - - - - - - - - - -
           Making Choices for Chain      0
 - - - - - - - - - - - - - - - - - - - - - - - - - - -

Completing residues with multiple options available, and solvent molecules

Checking positions of newly added atoms

Making choice for which molecules should be QM, which MM

Residues belonging to chain  0

Solvent molecules (SOL/HOH) belonging to this chain:
    1

Give the number of the molecule to be put in QM region (or 'c' to continue):

1

Putting HOH    1 in QM region

Give the number of the molecule to be put in QM region (or 'c' to continue):

c

Do you want to add solvent to your system (Y/n) ?

进入

Solvent (box) available:
   1:  HOH     HOH  Water molecule
   2:  MOH     MOH  Methanol molecule
   3:  CHL     CHL  Chloroform molecule

2

Reading contents of solvent box p2abox.MOH

Box Shape options:
 1  Spherical box
 2  Cubic box
Make a choice:

1

Writing inputfile for chain   0

Using total 收费   0.0 and total spin   0.0

Maximum atomic distance (Angs) from center        0.92
Give boxsize (def.:    15.00 Angs)

14.0

Using BOXSIZE value of  14.0000
Adding atoms for box     1  Added (Box):    84 (Total):    84  Excl. (1):   660  Excl. (2):     6
Adding atoms for box     2  Added (Box):   102 (Total):   186  Excl. (1):   642  Excl. (2):     6
Adding atoms for box     3  Added (Box):   102 (Total):   288  Excl. (1):   642  Excl. (2):     6
Adding atoms for box     4  Added (Box):   108 (Total):   396  Excl. (1):   642  Excl. (2):     0
Adding atoms for box     5  Added (Box):   120 (Total):   516  Excl. (1):   630  Excl. (2):     0
Adding atoms for box     6  Added (Box):    96 (Total):   612  Excl. (1):   654  Excl. (2):     0
Adding atoms for box     7  Added (Box):   108 (Total):   720  Excl. (1):   642  Excl. (2):     0
Adding atoms for box     8  Added (Box):   102 (Total):   822  Excl. (1):   642  Excl. (2):     6

Inputfile(s) written, everything processed, work has been done.
Thank you for using the PDB2ADF program.

================================
Normal ending of PDB2ADF program
================================

PDB2ADF生成的HOH.PDB2ADF文件的内容

该文件未完全赠送,因为它包含超过800个原子。

#! /bin/sh

$AMSBIN/ams << eor
System
  Charge   0.0
  Atoms
    O      2.4390    25.7950    11.6340 region=QM ForceField.Charge=-.834000   ForceField.Type=OW   !     1 HOH      1 O   
    H      1.7160    26.2820    11.2390 region=QM ForceField.Charge=.417000    ForceField.Type=HW   !     2 HOH      1 H1  
    H      3.1400    26.4400    11.7290 region=QM ForceField.Charge=.417000    ForceField.Type=HW   !     3 HOH      1 H2  
    C    -10.0667    22.2493    11.7437 region=MM ForceField.Charge=.116600    ForceField.Type=CT   !     4 MOH     1 C1  
    H    -10.2077    21.5053    10.9597 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !     5 MOH     1 HC1 
    H    -10.5047    21.8683    12.6667 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !     6 MOH     1 HC2 
    H    -10.5167    23.2103    11.4977 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !     7 MOH     1 HC3 
    O     -8.7387    22.3983    12.0617 region=MM ForceField.Charge=-.649700   ForceField.Type=OH   !     8 MOH     1 O1  
    H     -8.3007    22.6943    11.2607 region=MM ForceField.Charge=.421500    ForceField.Type=HO   !     9 MOH     1 HO1 
    C     -0.2827    19.0253     2.2847 region=MM ForceField.Charge=.116600    ForceField.Type=CT   !    10 MOH     2 C1  
    H     -0.5357    18.2063     2.9567 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !    11 MOH     2 HC1 
    H      0.7633    19.2913     2.4407 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !    12 MOH     2 HC2 
    H     -0.9267    19.8753     2.5107 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !    13 MOH     2 HC3 
    O     -0.4997    18.6373     0.9467 region=MM ForceField.Charge=-.649700   ForceField.Type=OH   !    14 MOH     2 O1  
    H      0.1123    17.9313     0.7287 region=MM ForceField.Charge=.421500    ForceField.Type=HO   !    15 MOH     2 HO1 
    ...
    C      6.1721    28.5021    18.9485 region=MM ForceField.Charge=.116600    ForceField.Type=CT   !   820 MOH   137 C1  
    H      7.1011    27.9431    18.8355 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !   821 MOH   137 HC1 
    H      6.3621    29.4771    19.3985 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !   822 MOH   137 HC2 
    H      5.4711    27.9401    19.5645 region=MM ForceField.Charge=.037200    ForceField.Type=H1   !   823 MOH   137 HC3 
    O      5.5611    28.7181    17.7095 region=MM ForceField.Charge=-.649700   ForceField.Type=OH   !   824 MOH   137 O1  
    H      5.2631    27.8621    17.3935 region=MM ForceField.Charge=.421500    ForceField.Type=HO   !   825 MOH   137 HO1 
  End

  BondOrders
        1      2 1.0
        1      3 1.0
        4      5 1.0
        4      6 1.0
        4      7 1.0
        4      8 1.0
        8      9 1.0
       10     11 1.0
       10     12 1.0
       10     13 1.0
       10     14 1.0
       14     15 1.0
      ...
      820    821 1.0
      820    822 1.0
      820    823 1.0
      820    824 1.0
      824    825 1.0
  End
End

Task GeometryOptimization

GeometryOptimization
  MaxIterations 100
  Convergence Gradients=1e-3
End
Engine Hybrid
  QMMM QMRegion=QM QMEngineID=ADF MMEngineID=ForceField

  Capping
    AtomicInfoForCappingAtom ForceField.Type=H1 ForceField.Charge=0.0
  End
  Engine ADF
    Title QM/MM calculation setup by pdb2adf: M.Swart et al., 2020
    Symmetry NOSYM

    Eprint
      SFO NOEIG NOOVL
    End

    XC
      GGA BP86
    End

    Basis
      type TZP
      core small
    End

    SCF
      diis ok=0.01
      Converge 1.0e-5 1.0e-5
      Iterations 99
    End
  EndEngine
  Engine ForceField
    Type Amber95
    ForceFieldFile $AMSHOME/atomicdata/ForceFields/amber95.ff
  EndEngine
EndEngine
eor