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 2005.01
                              Written by: Marcel Swart, 2005

                         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福彩3d字迷,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:福彩3d字迷(NAT)的总数,分子/残基(Nmol)和蛋白质链数(NCHAINS)。

Please wait, making connection tables

此时,通过观察福彩3d字迷距离来制造福彩3d字迷之间的连接。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/连接到金属福彩3d字迷(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 Atoms 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硫福彩3d字迷(左侧)粘合的福彩3d字迷的信息,以及最接近的五个非键合福彩3d字迷(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 Atoms 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 Atoms 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氮福彩3d字迷的信息。还表明(通过HB)是与另外的福彩3d字迷存在氢键。这里使用的定义是,如果它们都是非碳/非氢福彩3d字迷,则两个福彩3d字迷是氢键合,并且它们之间的距离小于福彩3d字迷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福彩3d字迷的最大距离。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个福彩3d字迷(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.)。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 2005.01
                              Written by: Marcel Swart, 2005

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

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

进入

Please give name of PDB-file

1dyz.pdb.

 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 Atoms 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 Atoms 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 Atoms 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 Atoms 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 Atoms 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 Atoms 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 Atoms 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 Atoms 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 Atoms 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 Atoms 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 Atoms 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 Atoms 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 Atoms 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 charge 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 charge   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
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个福彩3d字迷。

#! /bin/sh

$ADFBIN/adf << eor
TITLE QM/MM calculation setup by pdb2adf: M.Swart, 2005

Symmetry NOSYM

EPRINT
  SFO NOEIG NOOVL
END

XC
 GGA Becke-Perdew
END

GEOMETRY
 CONVERGE grad=1.0e-3 rad=1.0e-1
END

BASIS
 type TZP
 core small
END

SCF
 Converge 1.0e-5 1.0e-5
 Iterations 99
END

INTEGRATION 5.0 5.0 5.0

CHARGE   1.0  1.0
UNRESTRICTED

ATOMS
     1 C     11.3760     8.5410    29.7530
     2 H     10.9114     9.3322    30.3413
     3 H     12.4602     8.6423    29.8009
     4 C     10.9630     8.7450    28.3090
     5 O     10.8510     7.7910    27.5300
     6 N     10.6890     9.9800    27.9260
     7 H     10.7572    10.7382    28.5898
     8 C     10.2900    10.2500    26.5530
     9 H     10.5517     9.3991    25.9240
    10 C      8.7770    10.5120    26.4440
    11 H      8.5050    11.3473    27.0893
    12 H      8.5229    10.7532    25.4118
    13 C      7.9110     9.3590    26.8430
    14 N      8.0710     8.0910    26.3490
    15 C      7.1230     7.3010    26.8370
    16 H      7.0894     6.2496    26.5516
    17 N      6.3580     8.0230    27.6330
    18 H      5.5568     7.6742    28.1395
    19 C      6.8210     9.3110    27.6620
    20 H      6.3141    10.0588    28.2719
    21 C     11.0290     8.8020    20.9600
    22 H     11.3902     9.8061    21.1823
    23 C     10.0620     8.3640    22.0630
    24 H      9.2477     9.0845    22.1402
    25 H      9.6557     7.3817    21.8218
    26 S     10.8340     8.2410    23.7100
    27 C     10.1650     3.3080    22.4340
    28 H      9.2929     2.7403    22.7584
    29 C     10.1750     4.6030    23.2620
    30 H     11.1220     5.1220    23.1143
    31 H      9.3551     5.2459    22.9418
    32 C     10.0160     4.3980    24.7440
    33 N      9.7040     5.4090    25.6080
    34 C      9.6570     4.9300    26.8540
    35 H      9.4228     5.5952    27.6851
    36 N      9.9280     3.6450    26.8000
    37 H      9.9617     3.0260    27.5974
    38 C     10.1580     3.2710    25.4990
    39 H     10.3982     2.2340    25.2644
    40 C      6.0350     6.2800    19.5280
    41 H      4.9702     6.5113    19.5559
    42 C      6.6730     6.7710    20.8330
    43 H      7.7511     6.6157    20.7919
    44 H      6.4641     7.8329    20.9631
    45 C      6.1560     6.0500    22.0720
    46 H      5.0693     6.1257    22.1101
    47 H      6.4453     5.0000    22.0292
    48 S      6.7760     6.6970    23.6140
    49 C      6.0690     8.3070    23.6050
    50 H      4.9825     8.2271    23.5709
    51 H      6.3654     8.8396    24.5086
    52 H      6.4202     8.8537    22.7299
    53 CU     9.5640     7.3450    25.1750
    54 N     10.9860     7.2480    30.2860
    55 C     10.9790    11.4950    26.0450
    56 N     10.3490     8.8040    19.6720
    57 C     12.2010     7.8400    20.8870
    58 N     11.3800     2.5190    22.6730
    59 C      9.8250     3.6710    20.9970
    60 N      6.2160     4.8460    19.4030
    61 C      6.6330     7.0040    18.3530
    62 N     -1.1930    25.6890    17.1840
    63 H     -0.3133    25.1929    17.1970
    64 H     -1.3738    25.1438    18.0148
    65 H     -1.5170    24.8559    16.7138
    66 C     -1.4820    27.1340    16.8960
    67 H     -2.1350    27.2082    16.0264
    68 C     -2.1950    27.7860    18.0880
    69 H     -1.5602    27.7210    18.9717
    70 H     -2.3971    28.8331    17.8627
    71 H     -3.1350    27.2677    18.2776
    72 C     -0.1820    27.8790    16.5880
    73 O      0.8890    27.4920    17.0690
    74 N     -0.2890    28.9420    15.7940
    75 H     -1.1936    29.2105    15.4339
    76 C      0.8750    29.7430    15.4220
    77 H      0.5616    30.5606    14.7728
    78 C      1.5270    30.3290    16.6860
...
  9746 O     31.1328    34.4612    22.6903
  9747 H     31.8908    34.5740    22.1167
  9748 H     30.6706    35.2981    22.6446
END

QMMM
  FORCE_FIELD_FILE $ADFRESOURCES/ForceFields/amber95.ff
  RESTART_FILE mm.restart  ! old style restart
  OUTPUT_LEVEL=1
  WARNING_LEVEL=0
  ! -------------------
  ! for AddRemove model
  ! -------------------
  PARTITION=5
  ELSTAT_COUPLING_MODEL=4 ! for AddRemove model
 
  OPTIMIZE
    METHOD CONJGRAD
    MAX_STEPS 5000
    PRINT_CYCLES 10
    MM_NOTCONVERGED 0
  SUBEND

  LINK_BONDS
        1 -    54   1.3320 H H1
        8 -    55   1.3861 H H1
       21 -    56   1.3362 H H1
       21 -    57   1.3927 H H1
       27 -    58   1.3471 H H1
       27 -    59   1.3951 H H1
       40 -    60   1.3310 H H1
       40 -    61   1.3799 H H1
  SUBEND

  MM_CONNECTION_TABLE
        1 CT  QM    54     4     2     3
        2 H1  QM     1
        3 H1  QM     1
        4 C   QM     1     5     6
        5 O   QM     4
        6 N   QM     8     4     7
        7 H   QM     6
        8 CT  QM     6    10    55     9
        9 H1  QM     8
       10 CT  QM     8    13    11    12
       11 HC  QM    10
       12 HC  QM    10
       13 CC  QM    10    14    19
       14 NB  QM    13    15    53
       15 CR  QM    14    17    16
       16 H5  QM    15
       17 NA  QM    15    19    18
       18 H   QM    17
       19 CW  QM    13    17    20
       20 H4  QM    19
       21 CT  QM    56    23    57    22
       22 H1  QM    21
       23 CT  QM    21    26    24    25
       24 H1  QM    23
       25 H1  QM    23
       26 SH  QM    23    53
       27 CT  QM    58    29    59    28
       28 H1  QM    27
       29 CT  QM    27    32    30    31
       30 HC  QM    29
       31 HC  QM    29
       32 CC  QM    29    33    38
       33 NB  QM    32    34    53
       34 CR  QM    33    36    35
       35 H5  QM    34
       36 NA  QM    34    38    37
       37 H   QM    36
       38 CW  QM    32    36    39     
       39 H4  QM    38
       40 CT  QM    60    42    61    41
       41 H1  QM    40     
       42 CT  QM    40    45    43    44
       43 HC  QM    42     
       44 HC  QM    42
       45 CT  QM    42    48    46    47
       46 H1  QM    45
       47 H1  QM    45    
       48 S   QM    45    49
       49 CT  QM    48    50    51    52
       50 H1  QM    49    
       51 H1  QM    49    
       52 H1  QM    49    
       53 CU  QM    14    26    33
       54 N   LI     1   748   750
       55 C   LI     8   751   752
       56 N   LI    21  1683  1685
       57 C   LI    21  1686  1687
       58 N   LI    27  1737  1739    
       59 C   LI    27  1740  1741
       60 N   LI    40  1790  1792    
       61 C   LI    40  1793  1794
       62 N3  MM    66    63    64    65
       63 H   MM    62
       64 H   MM    62
       65 H   MM    62
       66 CT  MM    62    68    72    67
       67 HP  MM    66
       68 CT  MM    66    69    70    71
       69 HC  MM    68
       70 HC  MM    68
       71 HC  MM    68
       72 C   MM    66    73    74
       73 O   MM    72
       74 N   MM    76    72    75
       75 H   MM    74
       76 CT  MM    74    78    89    77
       77 H1  MM    76
       78 CT  MM    76    81    79    80
....
     9746 OW  MM  9747  9748
     9747 HW  MM  9746    
     9748 HW  MM  9746
  SUBEND
       
  CHARGES 
        1  -0.0252  
        2   0.0698  
        3   0.0698  
        4   0.5973  
        5  -0.5679  
        6  -0.4157  
        7   0.2719  
        8  -0.0581  
        9   0.1360  
       10  -0.0074  
       11   0.0367  
       12   0.0367  
       13   0.1868  
       14  -0.5432  
       15   0.1635  
       16   0.1435  
       17  -0.2795  
       18   0.3339
       19  -0.2207
       20   0.1862
       21   0.0350
       22   0.0480
       23  -0.7360
       24   0.2440
       25   0.2440
       26  -0.7360
       27  -0.0581
       28   0.1360
       29  -0.0074
       30   0.0367
       31   0.0367
       32   0.1868
       33  -0.5432
       34   0.1635
       35   0.1435
       36  -0.2795
       37   0.3339
       38  -0.2207
       39   0.1862
       40  -0.0237
       41   0.0880
       42   0.0342
       43   0.0241
       44   0.0241
       45   0.0018
       46   0.0440
       47   0.0440
       48  -0.2737
       49  -0.0536
       50   0.0684
       51   0.0684
       52   0.0684
       53   2.0000
       54  -0.4157
       55   0.5973
       56  -0.4630
       57   0.6160
       58  -0.4157
       59   0.5973
       60  -0.4157
       61   0.5973
       62   0.1414
       63   0.1997
       64   0.1997
       65   0.1997
       66   0.0962
       67   0.0889
       68  -0.0597
       69   0.0300
       70   0.0300
       71   0.0300
       72   0.6163
       73  -0.5722
       74  -0.4157
       75   0.2719
       76  -0.0031
       77   0.0850
       78  -0.0036
....
     9746  -0.8340
     9747   0.4170
     9748   0.4170
  SUBEND
END    
       
COMMENT
  Atom  ADF ID  p2a ID  Amber     Mol   Nr   Amber    pdb ID    atom
    C        1     828     CT     GLY   45     GLY       338     CA
    H        2     829     H1     GLY   45     GLY         0     HA2
    H        3     830     H1     GLY   45     GLY         0     HA3
    C        4     831     C      GLY   45     GLY       339     C
    O        5     832     O      GLY   45     GLY       340     O
    N        6     836     N      HIS   46     HIE       341     N
    H        7     837     H      HIS   46     HIE         0     H
    C        8     838     CT     HIS   46     HIE       342     CA
    H        9     839     H1     HIS   46     HIE         0     HA
    C       10     840     CT     HIS   46     HIE       345     CB
    H       11     841     HC     HIS   46     HIE         0     HB2
    H       12     842     HC     HIS   46     HIE         0     HB3
    C       13     843     CC     HIS   46     HIE       346     CG
    N       14     844     NB     HIS   46     HIE       347     ND1
    C       15     846     CR     HIS   46     HIE       349     CE1
    C       15     846     CR     HIS   46     HIE       349     CE1
    H       16     847     H5     HIS   46     HIE         0     HE1
    N       17     848     NA     HIS   46     HIE       350     NE2
    H       18     849     H      HIS   46     HIE         0     HE2
    C       19     850     CW     HIS   46     HIE       348     CD2
    H       20     851     H4     HIS   46     HIE         0     HD2
    C       21    1996     CT     CYS  112     CYM       824     CA
    H       22    1997     H1     CYS  112     CYM         0     HA
    C       23    1998     CT     CYS  112     CYM       827     CB
    H       24    1999     H1     CYS  112     CYM         0     HB3
    H       25    2000     H1     CYS  112     CYM         0     HB2
    S       26    2001     SH     CYS  112     CYM       828     SG
    C       27    2074     CT     HIS  117     HIE       858     CA
    H       28    2075     H1     HIS  117     HIE         0     HA
    C       29    2076     CT     HIS  117     HIE       861     CB
    H       30    2077     HC     HIS  117     HIE         0     HB2
    H       31    2078     HC     HIS  117     HIE         0     HB3
    C       32    2079     CC     HIS  117     HIE       862     CG
    N       33    2080     NB     HIS  117     HIE       863     ND1
    C       34    2082     CR     HIS  117     HIE       865     CE1
    H       35    2083     H5     HIS  117     HIE         0     HE1
    N       36    2084     NA     HIS  117     HIE       866     NE2
    H       37    2085     H      HIS  117     HIE         0     HE2
    C       38    2086     CW     HIS  117     HIE       864     CD2
    H       39    2087     H4     HIS  117     HIE         0     HD2
    C       40    2155     CT     MET  121     MET       895     CA
    H       41    2156     H1     MET  121     MET         0     HA
    C       42    2157     CT     MET  121     MET       898     CB
    H       43    2158     HC     MET  121     MET         0     HB2
    H       44    2159     HC     MET  121     MET         0     HB3
    C       45    2160     CT     MET  121     MET       899     CG
    H       46    2161     H1     MET  121     MET         0     HG2
    H       47    2162     H1     MET  121     MET         0     HG3
    S       48    2163     S      MET  121     MET       900     SD
    C       49    2164     CT     MET  121     MET       901     CE
    H       50    2165     H1     MET  121     MET         0     HE1
    H       51    2166     H1     MET  121     MET         0     HE2
    H       52    2167     H1     MET  121     MET         0     HE3
    CU      53    2318     CU     CU   130               959     CU 
    N       54     826     N      GLY   45     GLY       337     N  
    C       55     852     C      HIS   46     HIE       343     C  
    N       56    1994     N      CYS  112     CYM       823     N  
    C       57    2003     C      CYS  112     CYM       825     C  
    N       58    2072     N      HIS  117     HIE       857     N 
    C       59    2088     C      HIS  117     HIE       859     C 
    N       60    2153     N      MET  121     MET       894     N 
    C       61    2168     C      MET  121     MET       896     C  
    N       62       1     N3     ALA    1     ALA         1     N  
    H       63       2     H      ALA    1     ALA         0     H1
    H       64      11     H      ALA    1     ALA         0     H2
    H       65      12     H      ALA    1     ALA         0     H3
    C       66       3     CT     ALA    1     ALA         2     CA
    H       67       4     HP     ALA    1     ALA         0     HA 
    C       68       5     CT     ALA    1     ALA         5     CB 
    H       69       6     HC     ALA    1     ALA         0     HB1
    H       70       7     HC     ALA    1     ALA         0     HB2
    H       71       8     HC     ALA    1     ALA         0     HB3
    C       72       9     C      ALA    1     ALA         3     C  
    O       73      10     O      ALA    1     ALA         4     O  
    N       74      14     N      GLN    2     GLN         6     N  
    H       75      15     H      GLN    2     GLN         0     H  
    C       76      16     CT     GLN    2     GLN         7     CA 
    H       77      17     H1     GLN    2     GLN         0     HA
    C       78      18     CT     GLN    2     GLN        10     CB
....
    O     2111    2517     OW     HOH  196     SOL      1025     O
    H     2112    2518     HW     HOH  196     SOL         0     H1
    H     2113    2519     HW     HOH  196     SOL         0     H2
END

ENDINPUT
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.),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 2005.01
                              Written by: Marcel Swart, 2005

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

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

进入

Please give name of PDB-file

HOH.PDB.

 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 charge   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个福彩3d字迷。

#! /bin/sh

$ADFBIN/adf << eor
TITLE QM/MM calculation setup by pdb2adf: M.Swart, 2005

Symmetry NOSYM

EPRINT
  SFO NOEIG NOOVL
END

XC
 GGA Becke-Perdew
END

GEOMETRY
 CONVERGE grad=1.0e-3 rad=1.0e-1
END

BASIS
 type TZP
 core small
END

SCF
 Converge 1.0e-5 1.0e-5
 Iterations 99
END

INTEGRATION 5.0 5.0 5.0

CHARGE   0.0

ATOMS
     1 O      2.4390    25.7950    11.6340
     2 H      1.7160    26.2820    11.2390
     3 H      3.1400    26.4400    11.7290
     4 C    -10.0667    22.2493    11.7437
     5 H    -10.2077    21.5053    10.9597
     6 H    -10.5047    21.8683    12.6667
     7 H    -10.5167    23.2103    11.4977
     8 O     -8.7387    22.3983    12.0617
     9 H     -8.3007    22.6943    11.2607
    10 C     -0.2827    19.0253     2.2847
    11 H     -0.5357    18.2063     2.9567
    12 H      0.7633    19.2913     2.4407
    13 H     -0.9267    19.8753     2.5107
    14 O     -0.4997    18.6373     0.9467
    15 H      0.1123    17.9313     0.7287
....
   823 H      5.4711    27.9401    19.5645
   824 O      5.5611    28.7181    17.7095
   825 H      5.2631    27.8621    17.3935
END

QMMM
  FORCE_FIELD_FILE $ADFRESOURCES/ForceFields/amber95.ff
  RESTART_FILE mm.restart  ! old style restart
  OUTPUT_LEVEL=1
  WARNING_LEVEL=0
  ! -------------------
  ! for AddRemove model
  ! -------------------
  PARTITION=5
  ELSTAT_COUPLING_MODEL=4 ! for AddRemove model
 
  OPTIMIZE
    METHOD CONJGRAD
    MAX_STEPS 5000
    PRINT_CYCLES 10
    MM_NOTCONVERGED 0
  SUBEND

  MM_CONNECTION_TABLE
        1 OW  QM     2     3
        2 HW  QM     1
        3 HW  QM     1
        4 CT  MM     5     6     7     8
        5 H1  MM     4
        6 H1  MM     4
        7 H1  MM     4
        8 OH  MM     4     9
        9 HO  MM     8
       10 CT  MM    11    12    13    14
       11 H1  MM    10
       12 H1  MM    10
       13 H1  MM    10
       14 OH  MM    10    15
       15 HO  MM    14
....
      823 H1  MM   820
      824 OH  MM   820   825
      825 HO  MM   824
  SUBEND

  CHARGES
        1  -0.8340
        2   0.4170
        3   0.4170
        4   0.1166
        5   0.0372
        6   0.0372
        7   0.0372
        8  -0.6497
        9   0.4215
       10   0.1166
       11   0.0372
       12   0.0372
       13   0.0372
       14  -0.6497
       15   0.4215
...
      823   0.0372
      824  -0.6497
      825   0.4215
  SUBEND
END

COMMENT
  Atom  ADF ID  p2a ID  Amber     Mol   Nr   Amber    pdb ID    atom
    O        1       1     OW     HOH    1     SOL         2     O  
    H        2       2     HW     HOH    1     SOL         1     H1 
    H        3       3     HW     HOH    1     SOL         3     H2 
END

ENDINPUT
eor