alanin.psf

分子动力学计算程序

PSF 

      11 !NTITLE
 REMARKS FILENAME="/usr/people/nonella/xplor/benchmark1/ALANIN.PSF"             
 REMARKS PARAM11.PRO ( from PARAM6A )                                           
 REMARKS ===========                                                            
 REMARKS PROTEIN PARAMETERS:                                                    
 REMARKS PEPTIDE GEOMETRY FROM RAMACHANDRAN ET AL BBA 359:298 (1974)            
 REMARKS TORSIONS FROM HAGLER ET AL JACS 98:4600 (1976)                         
 REMARKS LENNARD-JONES NONBONDED PARAMETERS WITH SPECIAL TREATMENT OF 1:4       
 REMARKS CARBON-CARBON INTERACTIONS: JORGENSON ET. AL.                          
 REMARKS                           JACS 103:3976-3985 WITH 1-4 RC=1.80/0.1      
 REMARKS                                                                        
 REMARKS DATE:16-Feb-89  11:21:29       created by user: nonella                

      66 !NATOM
       1 MAIN 1    ACE  CA   CH3E   0.000000E+00   15.0350           0
       2 MAIN 1    ACE  C    C      0.450000       12.0110           0
       3 MAIN 1    ACE  O    O     -0.450000       15.9994           0
       4 MAIN 2    ALA  N    NH1   -0.350000       14.0067           0
       5 MAIN 2    ALA  H    H      0.250000       1.00800           0
       6 MAIN 2    ALA  CA   CH1E   0.100000       13.0190           0
       7 MAIN 2    ALA  CB   CH3E   0.000000E+00   15.0350           0
       8 MAIN 2    ALA  C    C      0.450000       12.0110           0
       9 MAIN 2    ALA  O    O     -0.450000       15.9994           0
      10 MAIN 3    ALA  N    NH1   -0.350000       14.0067           0
      11 MAIN 3    ALA  H    H      0.250000       1.00800           0
      12 MAIN 3    ALA  CA   CH1E   0.100000       13.0190           0
      13 MAIN 3    ALA  CB   CH3E   0.000000E+00   15.0350           0
      14 MAIN 3    ALA  C    C      0.450000       12.0110           0
      15 MAIN 3    ALA  O    O     -0.450000       15.9994           0
      16 MAIN 4    ALA  N    NH1   -0.350000       14.0067           0
      17 MAIN 4    ALA  H    H      0.250000       1.00800           0
      18 MAIN 4    ALA  CA   CH1E   0.100000       13.0190           0
      19 MAIN 4    ALA  CB   CH3E   0.000000E+00   15.0350           0
      20 MAIN 4    ALA  C    C      0.450000       12.0110           0
      21 MAIN 4    ALA  O    O     -0.450000       15.9994           0
      22 MAIN 5    ALA  N    NH1   -0.350000       14.0067           0
      23 MAIN 5    ALA  H    H      0.250000       1.00800           0
      24 MAIN 5    ALA  CA   CH1E   0.100000       13.0190           0
      25 MAIN 5    ALA  CB   CH3E   0.000000E+00   15.0350           0
      26 MAIN 5    ALA  C    C      0.450000       12.0110           0
      27 MAIN 5    ALA  O    O     -0.450000       15.9994           0
      28 MAIN 6    ALA  N    NH1   -0.350000       14.0067           0
      29 MAIN 6    ALA  H    H      0.250000       1.00800           0
      30 MAIN 6    ALA  CA   CH1E   0.100000       13.0190           0
      31 MAIN 6    ALA  CB   CH3E   0.000000E+00   15.0350           0
      32 MAIN 6    ALA  C    C      0.450000       12.0110           0
      33 MAIN 6    ALA  O    O     -0.450000       15.9994           0
      34 MAIN 7    ALA  N    NH1   -0.350000       14.0067           0
      35 MAIN 7    ALA  H    H      0.250000       1.00800           0
      36 MAIN 7    ALA  CA   CH1E   0.100000       13.0190           0
      37 MAIN 7    ALA  CB   CH3E   0.000000E+00   15.0350           0
      38 MAIN 7    ALA  C    C      0.450000       12.0110           0
      39 MAIN 7    ALA  O    O     -0.450000       15.9994           0
      40 MAIN 8    ALA  N    NH1   -0.350000       14.0067           0
      41 MAIN 8    ALA  H    H      0.250000       1.00800           0
      42 MAIN 8    ALA  CA   CH1E   0.100000       13.0190           0
      43 MAIN 8    ALA  CB   CH3E   0.000000E+00   15.0350           0
      44 MAIN 8    ALA  C    C      0.450000       12.0110           0
      45 MAIN 8    ALA  O    O     -0.450000       15.9994           0
      46 MAIN 9    ALA  N    NH1   -0.350000       14.0067           0
      47 MAIN 9    ALA  H    H      0.250000       1.00800           0
      48 MAIN 9    ALA  CA   CH1E   0.100000       13.0190           0
      49 MAIN 9    ALA  CB   CH3E   0.000000E+00   15.0350           0
      50 MAIN 9    ALA  C    C      0.450000       12.0110           0
      51 MAIN 9    ALA  O    O     -0.450000       15.9994           0
      52 MAIN 10   ALA  N    NH1   -0.350000       14.0067           0
      53 MAIN 10   ALA  H    H      0.250000       1.00800           0
      54 MAIN 10   ALA  CA   CH1E   0.100000       13.0190           0
      55 MAIN 10   ALA  CB   CH3E   0.000000E+00   15.0350           0
      56 MAIN 10   ALA  C    C      0.450000       12.0110           0
      57 MAIN 10   ALA  O    O     -0.450000       15.9994           0
      58 MAIN 11   ALA  N    NH1   -0.350000       14.0067           0
      59 MAIN 11   ALA  H    H      0.250000       1.00800           0
      60 MAIN 11   ALA  CA   CH1E   0.100000       13.0190           0
      61 MAIN 11   ALA  CB   CH3E   0.000000E+00   15.0350           0
      62 MAIN 11   ALA  C    C      0.450000       12.0110           0
      63 MAIN 11   ALA  O    O     -0.450000       15.9994           0
      64 MAIN 12   CBX  N    NH1   -0.350000       14.0067           0
      65 MAIN 12   CBX  H    H      0.250000       1.00800           0
      66 MAIN 12   CBX  CA   CH3E   0.100000       15.0350           0

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

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

      31 !NPHI: dihedrals
       2       4       6       8       1       2       4       6
       8      10      12      14       4       6       8      10
       6       8      10      12      14      16      18      20
      10      12      14      16      12      14      16      18
      20      22      24      26      16      18      20      22
      18      20      22      24      26      28      30      32
      22      24      26      28      24      26      28      30
      32      34      36      38      28      30      32      34
      30      32      34      36      38      40      42      44
      34      36      38      40      36      38      40      42
      44      46      48      50      40      42      44      46
      42      44      46      48      50      52      54      56
      46      48      50      52      48      50      52      54
      56      58      60      62      52      54      56      58
      54      56      58      60      58      60      62      64
      60      62      64      66

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

      11 !NDON: donors
       4       5      10      11      16      17      22      23
      28      29      34      35      40      41      46      47
      52      53      58      59      64      65

      11 !NACC: acceptors
       3       2       9       8      15      14      21      20
      27      26      33      32      39      38      45      44
      51      50      57      56      63      62

       0 !NNB

       0       0       0       0       0       0       0       0
       0       0       0       0       0       0       0       0
       0       0       0       0       0       0       0       0
       0       0       0       0       0       0       0       0
       0       0       0       0       0       0       0       0
       0       0       0       0       0       0       0       0
       0       0       0       0       0       0       0       0
       0       0       0       0       0       0       0       0
       0       0

      33       0 !NGRP
       0       0       0       1       0       0       3       0       0
       6       0       0       7       0       0       9       0       0
      12       0       0      13       0       0      15       0       0
      18       0       0      19       0       0      21       0       0
      24       0       0      25       0       0      27       0       0
      30       0       0      31       0       0      33       0       0
      36       0       0      37       0       0      39       0       0
      42       0       0      43       0       0      45       0       0
      48       0       0      49       0       0      51       0       0
      54       0       0      55       0       0      57       0       0
      60       0       0      61       0       0      63       0       0