dna1.mol

分子动力学模拟程序

N7     -3.91700   -.15700   3.28043   14.0070    -.690    3.297     .837  NN4 
C8     -4.66000  -1.23100   3.20042   12.0110     .410    3.208     .502  CN4 
H8     -5.75300  -1.19500   3.08142    1.0080     .280    2.352     .092  HN3 
N9     -3.95200  -2.41200   3.28043   14.0070    -.100    3.297     .837  NN2 
#    7 nucl - from 193           T                                              
O3*    -6.01200  -6.35800   3.45042   15.9990    -.550    3.154     .636  ON2 
P      -5.86900  -6.70400   5.00041   30.9740    1.500    3.831    2.450  P   
O1P    -6.15300  -8.13500   5.22043   15.9990    -.800    3.030     .502  ON3 
O2P    -6.68700  -5.75200   5.79042   15.9990    -.800    3.030     .502  ON3 
O5*    -4.32300  -6.40900   5.25041   15.9990    -.550    3.154     .636  ON2 
C5*    -3.35100  -6.93300   4.31042   12.0110    -.080    3.876     .230  CN8 
H5*    -3.07300  -6.22600   3.51442    1.0080     .090    2.352     .092  HN7 
H5**   -3.75300  -7.82900   3.81541    1.0080     .090    2.352     .092  HN7 
O1*    -1.29300  -6.08400   5.25041   15.9990    -.400    3.154     .636  ON6 
C1*    -1.35800  -5.70100   6.61043   12.0110     .110    4.054     .084  CN6B
H1*     -.31300  -5.86800   6.91142    1.0080     .090    2.352     .092  HN6 
C2*    -2.31500  -6.64800   7.32042   12.0110    -.180    4.054     .084  CN6 
H2*    -3.30000  -6.18700   7.48743    1.0080     .090    2.352     .092  HN6 
H2**   -1.82500  -6.78700   8.29543    1.0080     .090    2.352     .092  HN6 
C3*    -2.24600  -7.88600   6.44043   12.0110     .010    4.054     .084  CN6 
H3*    -3.11400  -8.54700   6.58643    1.0080     .090    2.352     .092  HN6 
C4*    -2.07900  -7.30000   5.04042   12.0110     .110    4.054     .084  CN6 
H4*    -1.58000  -8.11800   4.50043    1.0080     .090    2.352     .092  HN6 
#               T-BASE   atom 211                                               
N1C    -1.77900  -4.27500   6.66042   14.0070    -.300    3.297     .837  NN2 
C2      -.78700  -3.32800   6.81042   12.0110     .570    3.208     .586  CN1 
O2       .39300  -3.61900   6.90042   15.9990    -.470    3.029     .502  ON1 
N3H    -1.22200  -2.01900   6.85042   14.0070    -.460    3.297     .837  NN2U
HN3     -.41500  -1.43900   6.95743    1.0080     .360     .400     .192  HN2 
C4     -2.52400  -1.58400   6.76042   12.0110     .540    3.208     .586  CN1 
O4     -2.79500   -.37800   6.81042   15.9990    -.490    3.029     .502  ON1 
C5     -3.49300  -2.64200   6.61043   12.0110    -.150    3.208     .754  CN3 
C5M    -4.92500  -2.21400   6.50043   12.0110    -.110    3.671     .234  CN9 
H5M1   -5.57800  -2.99000   6.89943    1.0080     .070    2.352     .092  HN7 
H5M2   -5.18300  -2.03800   5.45642    1.0080     .070    2.352     .092  HN7 
H5M3   -5.08400  -1.29400   7.06343    1.0080     .070    2.352     .092  HN7 
C6     -3.10500  -3.93200   6.56042   12.0110     .170    3.208     .754  CN3 
H6     -3.93300  -4.64500   6.43641    1.0080     .130    2.352     .092  HN3 
#    8 nucl - from 225         C                                                
O3*    -1.12700  -8.67700   6.83041   15.9990    -.550    3.154     .636  ON2 
P       -.80700  -8.87300   8.38041   30.9740    1.500    3.831    2.450  P   
O1P     -.19600 -10.19800   8.60042   15.9990    -.800    3.030     .502  ON3 
O2P    -2.02900  -8.58300   9.17043   15.9990    -.800    3.030     .502  ON3 
O5*      .27000  -7.72500   8.63041   15.9990    -.550    3.154     .636  ON2 
C5*     1.36400  -7.57800   7.69041   12.0110    -.080    3.876     .230  CN8 
H5*     1.17400  -6.84300   6.89442    1.0080     .090    2.352     .092  HN7 
H5**    1.56600  -8.53900   7.19542    1.0080     .090    2.352     .092  HN7 
O1*     2.53000  -5.68200   8.63041   15.9990    -.400    3.154     .636  ON6 
C1*     2.25200  -5.41000   9.99042   12.0110     .110    4.054     .084  CN6B
H1*     3.19600  -4.93200  10.29143    1.0080     .090    2.352     .092  HN6 
C2*     2.03500  -6.73900  10.70042   12.0110    -.180    4.054     .084  CN6 
H2*      .96700  -6.94500  10.86743    1.0080     .090    2.352     .092  HN6 
H2**    2.51200  -6.56300  11.67542    1.0080     .090    2.352     .092  HN6 
C3*     2.81800  -7.70100   9.82042   12.0110     .010    4.054     .084  CN6 
H3*     2.50400  -8.74500   9.96642    1.0080     .090    2.352     .092  HN6 
C4*     2.60800  -7.12800   8.42043   12.0110     .110    4.054     .084  CN6 
H4*     3.49300  -7.49600   7.88041    1.0080     .090    2.352     .092  HN6 
#                  base  C       atom 243                                       
N1C     1.07300  -4.50400  10.04042   14.0070    -.160    3.297     .837  NN2 
C2      1.30700  -3.13900  10.19043   12.0110     .530    3.208     .586  CN1 
O2      2.47400  -2.73800  10.28043   15.9990    -.480    3.029     .502  ON1C
N3       .24600  -2.29700  10.24042   14.0070    -.670    3.297     .837  NN3 
C4     -1.00600  -2.76300  10.14043   12.0110     .620    3.208     .586  CN2 
N4     -2.00500  -1.89600  10.19043   14.0070    -.580    3.297     .837  NN1 
H41    -1.86800   -.91200  10.29942    1.0080     .270     .400     .192  HN1 
H42    -2.96500  -2.16800  10.12242    1.0080     .310     .400     .192  HN1 
C5     -1.27200  -4.16000   9.99042   12.0110    -.100    3.208     .754  CN3 
H5     -2.30300  -4.53600   9.92043    1.0080     .100    2.352     .092  HN3 
C6      -.19200  -4.98600   9.94041   12.0110     .110    3.208     .754  CN3 
H6      -.31500  -6.07300   9.82642    1.0080     .050    2.352     .092  HN3 
#     9 nucl - from 255        A                                                
O3*     4.18900  -7.68200  10.21042   15.9990    -.550    3.154     .636  ON2 
P       4.56200  -7.65300  11.76042   30.9740    1.500    3.831    2.450  P   
O1P     5.83600  -8.36500  11.98042   15.9990    -.800    3.030     .502  ON3 
O2P     3.40400  -8.13700  12.55042   15.9990    -.800    3.030     .502  ON3 
O5*     4.75900  -6.09100  12.01042   15.9990    -.550    3.154     .636  ON2 
C5*     5.55800  -5.33000  11.07042   12.0110    -.080    3.876     .230  CN8 
H5*     4.97200  -4.84600  10.27441    1.0080     .090    2.352     .092  HN7 
H5**    6.28600  -5.98800  10.57542    1.0080     .090    2.352     .092  HN7 
O1*     5.38700  -3.11000  12.01042   15.9990    -.400    3.154     .636  ON6 
C1*     5.00200  -3.05300  13.37042   12.0110     .110    4.054     .084  CN6B
H1*     5.48400  -2.11100  13.67142    1.0080     .090    2.352     .092  HN6 
C2*     5.60800  -4.25600  14.08043   12.0110    -.180    4.054     .084  CN6 
H2*     4.86500  -5.05000  14.24742    1.0080     .090    2.352     .092  HN6 
H2**    5.89000  -3.83300  15.05542    1.0080     .090    2.352     .092  HN6 
C3*     6.80600  -4.57300  13.20042   12.0110     .010    4.054     .084  CN6 
H3*     7.16600  -5.60300  13.34642    1.0080     .090    2.352     .092  HN6 
C4*     6.30000  -4.23300  11.80042   12.0110     .110    4.054     .084  CN6 
H4*     7.23200  -4.01100  11.26042    1.0080     .090    2.352     .092  HN6 
#           ADENINE  9     atom 273                                             
N1       .85800   -.06100  13.81042   14.0070    -.740    3.297     .837  NN3A
C2      2.16000    .20400  13.80042   12.0110     .530    3.208     .502  CN4 
H2      2.39200   1.27400  13.91043    1.0080     .160    2.352     .092  HN3 
N3C     3.18100   -.61800  13.68042   14.0070    -.690    3.297     .837  NN3A
C4      2.74400  -1.88600  13.56042   12.0110     .310    3.208     .502  CN5 
C5      1.45200  -2.32400  13.56042   12.0110     .230    3.208     .502  CN5 
C6       .45400  -1.33500  13.69041   12.0110     .430    3.208     .586  CN2 
N6      -.85900  -1.61600  13.70042   14.0070    -.800    3.297     .837  NN1 
HN61   -1.21800  -2.54500  13.61642    1.0080     .400     .400     .192  HN1 
HN62   -1.56600   -.91400  13.79242    1.0080     .400     .400     .192  HN1 
N7      1.39000  -3.69700  13.41043   14.0070    -.630    3.297     .837  NN4 
C8      2.63600  -4.05900  13.34042   12.0110     .380    3.208     .502  CN4 
H8      2.97600  -5.09900  13.22742    1.0080     .180    2.352     .092  HN3 
N9      3.51500  -3.01300  13.42043   14.0070    -.160    3.297     .837  NN2 
#    10 nucl - from 287          G                                              
O3*     7.90400  -3.75300  13.59042   15.9990    -.550    3.154     .636  ON2 
P       8.18900  -3.51000  15.14043   30.9740    1.500    3.831    2.450  P   
O1P     9.63800  -3.33800  15.36041   15.9990    -.800    3.030     .502  ON3 
O2P     7.53600  -4.58200  15.93042   15.9990    -.800    3.030     .502  ON3 
O5*     7.43100  -2.13100  15.39043   15.9990    -.550    3.154     .636  ON2 
C5*     7.62900  -1.04500  14.45042   12.0110    -.080    3.876     .230  CN8 
H5*     6.87100   -.99800  13.65441    1.0080     .090    2.352     .092  HN7 
H5**    8.60500  -1.15000  13.95543    1.0080     .090    2.352     .092  HN7 
O1*     6.18600    .65000  15.39043   15.9990    -.400    3.154     .636  ON6 
C1*     5.84100    .47000  16.75043   12.0110     .110    4.054     .084  CN6B
H1*     5.67800   1.51500  17.05142    1.0080     .090    2.352     .092  HN6 
C2*     7.03900   -.14700  17.46041   12.0110    -.180    4.054     .084  CN6 
H2*     6.90400  -1.22600  17.62743    1.0080     .090    2.352     .092  HN6 
H2**    7.01900    .36100  18.43542    1.0080     .090    2.352     .092  HN6 
C3*     8.19400    .30100  16.58041   12.0110     .010    4.054     .084  CN6 
H3*     9.09100   -.32100  16.72643    1.0080     .090    2.352     .092  HN6 
C4*     7.58500    .27800  15.18042   12.0110     .110    4.054     .084  CN6 
H4*     8.20900   1.00600  14.64043    1.0080     .090    2.352     .092  HN6 
#                   G - base       atom 305                                     
N1H      .76200    .51600  17.19043   14.0070    -.380    3.297     .837  NN2G
HN1     -.23400    .55800  17.27243    1.0080     .280     .400     .192  HN2 
C2      1.65900   1.56400  17.19043   12.0110     .720    3.208     .586  CN2 
N2      1.13700   2.78700  17.32042   14.0070    -.640    3.297     .837  NN1 
HN21    1.69300   3.61800  17.32642    1.0080     .310     .400     .192  HN1 
HN22     .15600   2.95300  17.42043    1.0080     .330     .400     .192  HN1 
N3C     2.97400   1.40600  17.06042   14.0070    -.660    3.297     .837  NN3A
C4      3.32900    .09900  16.94041   12.0110     .140    3.208     .502  CN5 
C5      2.50300  -1.01100  16.94041   12.0110    -.080    3.208     .502  CN5 
C6      1.10600   -.84200  17.07042   12.0110     .550    3.208     .586  CN1 
O6       .22000  -1.69600  17.09042   15.9990    -.470    3.029     .502  ON1 
N7      3.26100  -2.17500  16.80043   14.0070    -.690    3.297     .837  NN4 
C8      4.49400  -1.74300  16.72043   12.0110     .410    3.208     .502  CN4 
H8      5.35700  -2.41500  16.60143    1.0080     .280    2.352     .092  HN3 
N9      4.61500   -.37100  16.80043   14.0070    -.100    3.297     .837  NN2 
#
#     reference
#
 3
       CHARMM force field                                                       
       A.D.McKerell, J.Wiorkiewicz-Kuczera, M.Karplus                           
       JACS, v.117, p.11946 (1995)                                              
#   Num. of bonds
 530
#ID(typ)    N1   N2   Reqv         Force          D        RHO (A**-1)
     0     1     2    1.6000   1125.00     .0000     .0000
     0     1   301    1.4300   1424.00     .0000     .0000
     0     2     3    1.4800   2417.00     .0000     .0000
     0     2     4    1.4800   2417.00     .0000     .0000
     0     2     5    1.6000   1125.00     .0000     .0000
     0     5     6    1.4300   1424.00     .0000     .0000
     0     6     7    1.1110   1294.00     .0000     .0000
     0     6     8    1.1110   1294.00     .0000     .0000
     0     6    17    1.5160    932.00     .0000     .0000
     0     9    10    1.4100   1242.00     .0000     .0000
     0     9    17    1.4450   1242.00     .0000     .0000
     0    10    11    1.1110   1294.00     .0000     .0000
     0    10    12    1.5270    932.00     .0000     .0000
     0    10    32    1.4800   1256.00     .0000     .0000
     0    12    13    1.1110   1294.00     .0000     .0000
     0    12    14    1.1110   1294.00     .0000     .0000
     0    12    15    1.5160    932.00     .0000     .0000
     0    15    16    1.1110   1294.00     .0000     .0000
     0    15    17    1.5160    932.00     .0000     .0000
     0    15    33    1.4300   1424.00     .0000     .0000
     0    17    18    1.1110   1294.00     .0000     .0000
     0    19    20    1.3100   1298.00     .0000     .0000
     0    19    25    1.3400   1340.00     .0000     .0000
     0    20    21    1.0900   1591.00     .0000     .0000
     0    20    22    1.3100   1298.00     .0000     .0000
     0    22    23    1.3360   1465.00     .0000     .0000
     0    23    24    1.3700   1340.00     .0000     .0000
     0    23    32    1.4080   1264.00     .0000     .0000
     0    24    25    1.3600   1264.00     .0000     .0000
     0    24    29    1.3600   1465.00     .0000     .0000
     0    25    26    1.3650   1675.00     .0000     .0000
     0    26    27    1.0000   2043.00     .0000     .0000
     0    26    28    1.0000   2043.00     .0000     .0000
     0    29    30    1.3080   1675.00     .0000     .0000
     0    30    31    1.0900   1591.00     .0000     .0000
     0    30    32    1.3650   1256.00     .0000     .0000
     0    33    34    1.6000   1125.00     .0000     .0000
     0    34    35    1.4800   2417.00     .0000     .0000
     0    34    36    1.4800   2417.00     .0000     .0000
     0    34    37    1.6000   1125.00     .0000     .0000
     0    37    38    1.4300   1424.00     .0000     .0000
     0    38    39    1.1110   1294.00     .0000     .0000
     0    38    40    1.1110   1294.00     .0000     .0000
     0    38    49    1.5160    932.00     .0000     .0000
     0    41    42    1.4100   1242.00     .0000     .0000
     0    41    49    1.4450   1242.00     .0000     .0000
     0    42    43    1.1110   1294.00     .0000     .0000
     0    42    44    1.5270    932.00     .0000     .0000
     0    42    51    1.4800   1256.00     .0000     .0000
     0    44    45    1.1110   1294.00     .0000     .0000
     0    44    46    1.1110   1294.00     .0000     .0000
     0    44    47    1.5160    932.00     .0000     .0000
     0    47    48    1.1110   1294.00     .0000     .0000
     0    47    49    1.5160    932.00     .0000     .0000
     0    47    65    1.4300   1424.00     .0000     .0000
     0    49    50    1.1110   1294.00     .0000     .0000
     0    51    52    1.4000   1264.00     .0000     .0000
     0    51    63    1.3650   1264.00     .0000     .0000
     0    52    53    1.2350   2596.00     .0000     .0000
     0    52    54    1.4100   1424.00     .0000     .0000
     0    54    55    1.0100   1985.00     .0000     .0000
     0    54    56    1.4100   1424.00     .0000     .0000
     0    56    57    1.2350   2596.00     .0000     .0000