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 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 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 name 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 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个原子。 请注意,如果环境变量SCM_PDB2ADF设置为Old,则使用旧样式QM / MM输入格式。 此示例使用默认的新格式。

#! /bin/sh

$ADFBIN/adf << eor
TITLE QM/MM calculation setup by pdb2adf: M.Swart, 2008

Symmetry NOSYM

EPRINT
  SFO NOEIG NOOVL
END

XC
 GGA Becke-Perdew
END

GEOMETRY
 iterations 100
 CONVERGE grad=1.0e-3 rad=0.1
END

BASIS
 type TZP
 core small
END

SCF
 diis ok=0.01
 Converge 1.0e-5 1.0e-5
 Iterations 99
END

CHARGE   1.0  1.0
UNRESTRICTED

ATOMS
     1 N     -1.1930    25.6890    17.1840
     2 H     -0.3133    25.1929    17.1970
     3 H     -1.3738    25.1438    18.0148
     4 H     -1.5170    24.8559    16.7138
     5 C     -1.4820    27.1340    16.8960
     6 H     -2.1350    27.2082    16.0264
     7 C     -2.1950    27.7860    18.0880
     8 H     -1.5602    27.7210    18.9717
     9 H     -2.3971    28.8331    17.8627
    10 H     -3.1350    27.2677    18.2776
    11 C     -0.1820    27.8790    16.5880
    12 O      0.8890    27.4920    17.0690
    13 N     -0.2890    28.9420    15.7940
    14 H     -1.1936    29.2105    15.4339
    15 C      0.8750    29.7430    15.4220
    16 H      0.5616    30.5606    14.7728
    17 C      1.5270    30.3290    16.6860
    18 H      0.7563    30.7529    17.3298
    19 H      2.0544    29.5402    17.2224
    20 C      2.5320    31.4280    16.4240
    21 H      2.9095    31.3405    15.4052
    22 H      2.0516    32.3982    16.5508
    23 C      3.7140    31.3600    17.3720
    24 O      4.5190    30.4170    17.3220
    25 N      3.8270    32.3530    18.2440
    26 H      4.5950    32.3600    18.9000
    27 H      3.1446    33.0976    18.2480
    28 C      1.8460    28.8170    14.6770
    29 O      1.4330    28.0490    13.7940
    30 N      3.1200    28.8760    15.0450
    31 H      3.4036    29.5187    15.7707
    32 C      4.1380    28.0400    14.4360
    33 H      3.6966    27.4628    13.6235
    34 C      5.2490    28.9240    13.8830
    35 H      5.5773    29.6209    14.6541
    36 H      6.0893    28.3021    13.5744
    37 S      4.6970    29.8870    12.4450
    38 C      4.6800    27.1010    15.5090
    39 O      5.8890    27.0060    15.7280
    40 N      3.7690    26.4380    16.2040
    41 H      2.7886    26.5676    15.9987
    42 C      4.1640    25.5320    17.2520
    43 H      5.0753    25.0110    16.9583
    44 C      4.4480    26.3010    18.5380
    45 H      4.7889    25.6090    19.3080
    46 H      5.2208    27.0470    18.3527
    47 C      3.2450    27.0350    19.0990
    48 H      2.6884    27.4975    18.2839
    49 H      2.6007    26.3297    19.6240
    50 C      3.6030    28.1430    20.0880
    51 O      4.7940    28.3110    20.4290
    52 O      2.6740    28.8670    20.5030
    53 C      3.0820    24.5140    17.4740
    54 O      1.9190    24.7350    17.1470
    55 N      3.4810    23.3770    18.0170
    56 H      4.4563    23.2437    18.2430
    57 C      2.5550    22.3010    18.3030
    58 H      1.5462    22.7037    18.3941
    59 C      2.5590    21.2690    17.1740
    60 H      3.5602    20.8520    17.0658
    61 H      1.8565    20.4695    17.4093
    62 H      2.2632    21.7490    16.2412
    63 C      2.9700    21.6650    19.6140
    64 O      4.1160    21.8010    20.0550
    65 N      2.0180    21.0240    20.2660
    66 H      1.0839    20.9887    19.8835
    67 C      2.2640    20.3560    21.5330
    68 H      3.3189    20.4450    21.7924
    69 C      1.4300    21.0100    22.6680
    70 H      0.3783    21.0286    22.3823
    71 C      1.5670    20.2160    23.9790
    72 H      2.6136    20.1931    24.2828
    73 H      0.9735    20.6946    24.7580
    74 H      1.2111    19.1971    23.8262
    75 O      1.8900    22.3550    22.8810
    76 H      1.3759    22.7617    23.5824
    77 C      1.9150    18.8760    21.4070
    78 O      0.8730    18.5150    20.8640
...
  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
  ELSTAT_COUPLING_MODEL=1

  LINK_BONDS
      691 -   689   1.3320 H H1
      698 -   711   1.3861 H H1
     1648 -  1646   1.3362 H H1
     1648 -  1654   1.3927 H H1
     1710 -  1708   1.3471 H H1
     1710 -  1723   1.3951 H H1
     1778 -  1776   1.3310 H H1
     1778 -  1791   1.3799 H H1
  SUBEND
  ! ---------------------------------------------------
  ! use NEWQMMM developer implementation
  !
  ! NOTE:
  ! the rest of QMMM block is only for use with NEWQMMM
  ! ---------------------------------------------------
  NEWQMMM
  QMMM_PREOPTIMIZE

  QM_INFO
      689    H1  LI   -0.055275  GLY    45  N       691    687    690
      691  CT    QM   -0.025200  GLY    45  CA      689    694    692    693
      692  H1    QM    0.069800  GLY    45  HA2     691
      693  H1    QM    0.069800  GLY    45  HA3     691
      694  C     QM    0.597300  GLY    45  C       691    695    696
      695  O     QM   -0.567900  GLY    45  O       694
      696  N     QM   -0.415700  HIS    46  N       698    694    697
      697  H     QM    0.271900  HIS    46  H       696
      698  CT    QM   -0.058100  HIS    46  CA      696    700    711    699
      699  H1    QM    0.136000  HIS    46  HA      698
      700  CT    QM   -0.007400  HIS    46  CB      698    703    701    702
      701  HC    QM    0.036700  HIS    46  HB2     700
      702  HC    QM    0.036700  HIS    46  HB3     700
      703  CC    QM    0.186800  HIS    46  CG      700    704    709
      704  NB    QM   -0.543200  HIS    46  ND1     703    705   1915
      705  CR    QM    0.163500  HIS    46  CE1     704    707    706
      706  H5    QM    0.143500  HIS    46  HE1     705
      707  NA    QM   -0.279500  HIS    46  NE2     705    709    708
      708  H     QM    0.333900  HIS    46  HE2     707
      709  CW    QM   -0.220700  HIS    46  CD2     703    707    710
      710  H4    QM    0.186200  HIS    46  HD2     709
      711    H1  LI   -0.055275  HIS    46  C       698    712    713
     1646    H1  LI   -0.055275  CYS   112  N      1648   1644   1647
     1648  CT    QM    0.035000  CYS   112  CA     1646   1650   1654   1649
     1649  H1    QM    0.048000  CYS   112  HA     1648
     1650  CT    QM   -0.736000  CYS   112  CB     1648   1653   1651   1652
     1651  H1    QM    0.244000  CYS   112  HB3    1650
     1652  H1    QM    0.244000  CYS   112  HB2    1650
     1653  SH    QM   -0.736000  CYS   112  SG     1650   1915
     1654    H1  LI   -0.055275  CYS   112  C      1648   1655   1656
     1708    H1  LI   -0.055275  HIS   117  N      1710   1706   1709
     1710  CT    QM   -0.058100  HIS   117  CA     1708   1712   1723   1711
     1711  H1    QM    0.136000  HIS   117  HA     1710
     1712  CT    QM   -0.007400  HIS   117  CB     1710   1715   1713   1714
     1713  HC    QM    0.036700  HIS   117  HB2    1712
     1714  HC    QM    0.036700  HIS   117  HB3    1712
     1715  CC    QM    0.186800  HIS   117  CG     1712   1716   1721
     1716  NB    QM   -0.543200  HIS   117  ND1    1715   1717   1915
     1717  CR    QM    0.163500  HIS   117  CE1    1716   1719   1718
     1718  H5    QM    0.143500  HIS   117  HE1    1717
     1719  NA    QM   -0.279500  HIS   117  NE2    1717   1721   1720
     1720  H     QM    0.333900  HIS   117  HE2    1719
     1721  CW    QM   -0.220700  HIS   117  CD2    1715   1719   1722
     1722  H4    QM    0.186200  HIS   117  HD2    1721
     1723    H1  LI   -0.055275  HIS   117  C      1710   1724   1725
     1776    H1  LI   -0.055275  MET   121  N      1778   1774   1777
     1778  CT    QM   -0.023700  MET   121  CA     1776   1780   1791   1779
     1779  H1    QM    0.088000  MET   121  HA     1778
     1780  CT    QM    0.034200  MET   121  CB     1778   1783   1781   1782
     1781  HC    QM    0.024100  MET   121  HB2    1780
     1782  HC    QM    0.024100  MET   121  HB3    1780
     1783  CT    QM    0.001800  MET   121  CG     1780   1786   1784   1785
     1784  H1    QM    0.044000  MET   121  HG2    1783
     1785  H1    QM    0.044000  MET   121  HG3    1783
     1786  S     QM   -0.273700  MET   121  SD     1783   1787
     1787  CT    QM   -0.053600  MET   121  CE     1786   1788   1789   1790
     1788  H1    QM    0.068400  MET   121  HE1    1787
     1789  H1    QM    0.068400  MET   121  HE2    1787
     1790  H1    QM    0.068400  MET   121  HE3    1787
     1791    H1  LI   -0.055275  MET   121  C      1778   1792   1793
     1915  CU    QM    2.000000  CU    130  CU      704   1653   1716
  SUBEND

  QMMM_INFO
        1  N3    MM    0.141400  ALA     1  N         5      2      3      4
        2  H     MM    0.199700  ALA     1  H1        1
        3  H     MM    0.199700  ALA     1  H2        1
        4  H     MM    0.199700  ALA     1  H3        1
        5  CT    MM    0.096200  ALA     1  CA        1      7     11      6
        6  HP    MM    0.088900  ALA     1  HA        5
        7  CT    MM   -0.059700  ALA     1  CB        5      8      9     10
        8  HC    MM    0.030000  ALA     1  HB1       7
        9  HC    MM    0.030000  ALA     1  HB2       7
       10  HC    MM    0.030000  ALA     1  HB3       7
       11  C     MM    0.616300  ALA     1  C         5     12     13
       12  O     MM   -0.572200  ALA     1  O        11
       13  N     MM   -0.415700  GLN     2  N        15     11     14
       14  H     MM    0.271900  GLN     2  H        13
       15  CT    MM   -0.003100  GLN     2  CA       13     17     28     16
       16  H1    MM    0.085000  GLN     2  HA       15
       17  CT    MM   -0.003600  GLN     2  CB       15     20     18     19
       ...
     9746  OW    MM   -0.834000  HOH  2545  O      9747   9748
     9747  HW    MM    0.417000  HOH  2545  H1     9746
     9748  HW    MM    0.417000  HOH  2545  H2     9746
  SUBEND
END

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 name 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 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个原子。 请注意,如果环境变量SCM_PDB2ADF设置为Old,则使用旧样式QM / MM输入格式。 此示例使用默认的新格式。

#! /bin/sh

$ADFBIN/adf << eor
TITLE QM/MM calculation setup by pdb2adf: M.Swart, 2008

Symmetry NOSYM

EPRINT
  SFO NOEIG NOOVL
END

XC
 GGA Becke-Perdew
END

GEOMETRY
 iterations 100
 CONVERGE grad=1.0e-3 rad=0.1
END

BASIS
 type TZP
 core small
END

SCF
 diis ok=0.01
 Converge 1.0e-5 1.0e-5
 Iterations 99
END

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
  ELSTAT_COUPLING_MODEL=1
  ! ---------------------------------------------------
  ! use NEWQMMM developer implementation
  !
  ! NOTE:
  ! the rest of QMMM block is only for use with NEWQMMM
  ! ---------------------------------------------------
  NEWQMMM
  QMMM_PREOPTIMIZE

  QM_INFO
        1  OW    QM   -0.834000  HOH     1  O         2      3
        2  HW    QM    0.417000  HOH     1  H1        1
        3  HW    QM    0.417000  HOH     1  H2        1
  SUBEND

  QMMM_INFO
        1  OW    QM   -0.834000  HOH     1  O         2      3
        2  HW    QM    0.417000  HOH     1  H1        1
        3  HW    QM    0.417000  HOH     1  H2        1
        4  CT    MM    0.116600  MOH     1  C1        5      6      7      8
        5  H1    MM    0.037200  MOH     1  HC1       4
        6  H1    MM    0.037200  MOH     1  HC2       4
        7  H1    MM    0.037200  MOH     1  HC3       4
        8  OH    MM   -0.649700  MOH     1  O1        4      9
        9  HO    MM    0.421500  MOH     1  HO1       8
       10  CT    MM    0.116600  MOH     2  C1       11     12     13     14
       11  H1    MM    0.037200  MOH     2  HC1      10
       12  H1    MM    0.037200  MOH     2  HC2      10
       13  H1    MM    0.037200  MOH     2  HC3      10
       14  OH    MM   -0.649700  MOH     2  O1       10     15
       15  HO    MM    0.421500  MOH     2  HO1      14
....
      823  H1    MM    0.037200  MOH   137  HC3     820
      824  OH    MM   -0.649700  MOH   137  O1      820    825
      825  HO    MM    0.421500  MOH   137  HO1     824
  SUBEND
END
eor