[X-plor] how to create paramerter file for charmm simulations

saravana prakash saravanprakash at yahoo.com
Tue Aug 15 10:53:24 EST 2006


Skipped content of type multipart/alternative-------------- next part --------------
PSF

       3 !NTITLE
 REMARKS original generated structure x-plor psf file
 REMARKS topology SARCOrigina153_autopsf-temp.top 
 REMARKS segment O1 { first NONE; last NONE; auto angles dihedrals }

      36 !NATOM
       1 O1   1    FRAG N1   NX    -0.280000       14.0067           0
       2 O1   1    FRAG C2   CT    -0.063000       12.0110           0
       3 O1   1    FRAG C3   CT    -0.121000       12.0110           0
       4 O1   1    FRAG C4   CT    -0.010000       12.0110           0
       5 O1   1    FRAG C5   CUA1   0.437000       12.0110           0
       6 O1   1    FRAG C6   CUA1   0.230000       12.0110           0
       7 O1   1    FRAG C7   CUA1  -0.298000       12.0110           0
       8 O1   1    FRAG C8   C      0.437000       12.0110           0
       9 O1   1    FRAG C9   CUA1  -0.207000       12.0110           0
      10 O1   1    FRAG C10  CUA1  -0.285000       12.0110           0
      11 O1   1    FRAG O11  OE    -0.548000       15.9994           0
      12 O1   1    FRAG C12  C      1.067000       12.0110           0
      13 O1   1    FRAG C13  CUA1  -0.478000       12.0110           0
      14 O1   1    FRAG C14  CUA1  -0.073000       12.0110           0
      15 O1   1    FRAG C15  CT     0.089000       12.0110           0
      16 O1   1    FRAG C16  CT     0.006000       12.0110           0
      17 O1   1    FRAG C17  CT     0.019000       12.0110           0
      18 O1   1    FRAG O18  O      0.620000       15.9994           0
      19 O1   1    FRAG C19  CF3    1.357000       12.0110           0
      20 O1   1    FRAG F20  XF    -0.426000       18.9984           0
      21 O1   1    FRAG F21  XF    -0.431000       18.9984           0
      22 O1   1    FRAG F22  XF    -0.424000       18.9984           0
      23 O1   1    FRAG H23  HA     0.089000        1.0080           0
      24 O1   1    FRAG H24  HA     0.095000        1.0080           0
      25 O1   1    FRAG H25  HA     0.070000        1.0080           0
      26 O1   1    FRAG H26  HA     0.070000        1.0080           0
      27 O1   1    FRAG H27  HA     0.041000        1.0080           0
      28 O1   1    FRAG H28  HA     0.053000        1.0080           0
      29 O1   1    FRAG H29  HA     0.233000        1.0080           0
      30 O1   1    FRAG H30  HA     0.237000        1.0080           0
      31 O1   1    FRAG H31  HA     0.028000        1.0080           0
      32 O1   1    FRAG H32  HA     0.021000        1.0080           0
      33 O1   1    FRAG H33  HA     0.011000        1.0080           0
      34 O1   1    FRAG H34  HA     0.026000        1.0080           0
      35 O1   1    FRAG H35  HA     0.064000        1.0080           0
      36 O1   1    FRAG H36  HA     0.056000        1.0080           0

      39 !NBOND: bonds
       1       2       1       6       1      17       2       3
       2      23       2      24       3       4       3      25
       3      26       4       5       4      27       4      28
       5       6       5      10       6       7       7       8
       7      15       8       9       8      11       9      10
       9      14      10      29      11      12      12      13
      12      18      13      14      13      30      14      19
      15      16      15      31      15      32      16      17
      16      33      16      34      17      35      17      36
      19      20      19      21      19      22

      73 !NTHETA: angles
       1      17      36       1      17      35       1      17      16
       1       6       7       1       6       5       1       2      24
       1       2      23       1       2       3       2       3      26
       2       3      25       2       3       4       2       1      17
       2       1       6       3       4      28       3       4      27
       3       4       5       3       2      24       3       2      23
       4       5      10       4       5       6       4       3      26
       4       3      25       5      10      29       5      10       9
       5       6       7       5       4      28       5       4      27
       6       7      15       6       7       8       6       5      10
       6       1      17       7      15      32       7      15      31
       7      15      16       7       8      11       7       8       9
       8      11      12       8       9      14       8       9      10
       8       7      15       9      14      19       9      14      13
       9      10      29       9       8      11      10       9      14
      11      12      18      11      12      13      12      13      30
      12      13      14      13      14      19      13      12      18
      14      19      22      14      19      21      14      19      20
      14      13      30      15      16      34      15      16      33
      15      16      17      16      17      36      16      17      35
      16      15      32      16      15      31      17      16      34
      17      16      33      20      19      22      20      19      21
      21      19      22      23       2      24      25       3      26
      27       4      28      31      15      32      33      16      34
      35      17      36

     110 !NPHI: dihedrals
       1      17      16      15       1      17      16      33
       1      17      16      34       1       6       5       4
       1       6       5      10       1       6       7       8
       1       6       7      15       1       2       3       4
       1       2       3      25       1       2       3      26
       2       3       4       5       2       3       4      27
       2       3       4      28       2       1       6       5
       2       1       6       7       2       1      17      16
       2       1      17      35       2       1      17      36
       3       4       5       6       3       4       5      10
       3       2       1       6       3       2       1      17
       4       5       6       7       4       5      10       9
       4       5      10      29       4       3       2      23
       4       3       2      24       5      10       9       8
       5      10       9      14       5       6       1      17
       5       6       7       8       5       6       7      15
       5       4       3      25       5       4       3      26
       6       7       8       9       6       7       8      11
       6       7      15      16       6       7      15      31
       6       7      15      32       6       5       4      27
       6       5       4      28       6       5      10       9
       6       5      10      29       6       1       2      23
       6       1       2      24       6       1      17      16
       6       1      17      35       6       1      17      36
       7      15      16      17       7      15      16      33
       7      15      16      34       7       8       9      10
       7       8       9      14       7       8      11      12
       7       6       1      17       7       6       5      10
       8      11      12      13       8      11      12      18
       8       9      10      29       8       9      14      13
       8       9      14      19       8       7      15      16
       8       7      15      31       8       7      15      32
       9      14      13      12       9      14      13      30
       9      14      19      20       9      14      19      21
       9      14      19      22       9       8       7      15
       9       8      11      12      10       9       8      11
      10       9      14      13      10       9      14      19
      10       5       4      27      10       5       4      28
      11      12      13      14      11      12      13      30
      11       8       7      15      11       8       9      14
      12      13      14      19      13      14      19      20
      13      14      19      21      13      14      19      22
      14      13      12      18      14       9      10      29
      15      16      17      35      15      16      17      36
      17      16      15      31      17      16      15      32
      17       1       2      23      17       1       2      24
      18      12      13      30      19      14      13      30
      23       2       3      25      23       2       3      26
      24       2       3      25      24       2       3      26
      25       3       4      27      25       3       4      28
      26       3       4      27      26       3       4      28
      31      15      16      33      31      15      16      34
      32      15      16      33      32      15      16      34
      33      16      17      35      33      16      17      36
      34      16      17      35      34      16      17      36

       0 !NIMPHI: impropers


       0 !NDON: donors


       0 !NACC: acceptors


       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

       1       0 !NGRP
       0       0       0

-------------- next part --------------
* ...
* Insight II generated topology file for SARCORIGINA153
* Produced on Mon Aug 14 23:39:14 2006
*
   22    0
MASS    33 NX    14.00670 N 
MASS    10 CT    12.01100 C 
MASS    16 CUA1  12.01100 C 
MASS    14 C     12.01100 C 
MASS    50 OE    15.99940 O 
MASS    40 O     15.99940 O 
MASS   232 CF3   12.01100 C 
MASS    92 XF    18.99840 F 
MASS     3 HA     1.00800 H 

AUTO ANGLES DIHE


DEFAULT FIRST NONE LAST NONE


RESI FRAG	0.001
GROUP
ATOM N1   NX    -0.280
ATOM C2   CT    -0.063
ATOM C3   CT    -0.121
ATOM C4   CT    -0.010
ATOM C5   CUA1   0.437
ATOM C6   CUA1   0.230
ATOM C7   CUA1  -0.298
ATOM C8   C      0.437
ATOM C9   CUA1  -0.207
ATOM C10  CUA1  -0.285
ATOM O11  OE    -0.548
ATOM C12  C      1.067
ATOM C13  CUA1  -0.478
ATOM C14  CUA1  -0.073
ATOM C15  CT     0.089
ATOM C16  CT     0.006
ATOM C17  CT     0.019
ATOM O18  O      0.620
ATOM C19  CF3    1.357
ATOM F20  XF    -0.426
ATOM F21  XF    -0.431
ATOM F22  XF    -0.424
ATOM H23  HA     0.089
ATOM H24  HA     0.095
ATOM H25  HA     0.070
ATOM H26  HA     0.070
ATOM H27  HA     0.041
ATOM H28  HA     0.053
ATOM H29  HA     0.233
ATOM H30  HA     0.237
ATOM H31  HA     0.028
ATOM H32  HA     0.021
ATOM H33  HA     0.011
ATOM H34  HA     0.026
ATOM H35  HA     0.064
ATOM H36  HA     0.056
BOND N1   C2      N1   C6      N1   C17     C2   C3      C2   H23  
BOND C2   H24     C3   C4      C3   H25     C3   H26     C4   C5   
BOND C4   H27     C4   H28     C5   C6      C5   C10     C6   C7   
BOND C7   C8      C7   C15     C8   C9      C8   O11     C9   C10  
BOND C9   C14     C10  H29     O11  C12     C12  C13     C12  O18  
BOND C13  C14     C13  H30     C14  C19     C15  C16     C15  H31  
BOND C15  H32     C16  C17     C16  H33     C16  H34     C17  H35  
BOND C17  H36     C19  F20     C19  F21     C19  F22     
ACCEPTOR O11  C8  
ACCEPTOR O11  C12 
ACCEPTOR O18  C12 
IC C6   N1   C2   C3    1.3920  119.3801   49.2724  108.2697  1.5375
IC C6   N1   C2   H23   1.3920  119.3801  166.2319  110.8846  1.0952
IC C6   N1   C2   H24   1.3920  119.3801  -74.2566  109.9224  1.0865
IC C17  N1   C2   C3    1.4692  115.6335 -149.9597  108.2697  1.5375
IC C2   N1   C6   C5    1.4806  119.3801  -20.7341  119.5837  1.3867
IC C2   N1   C6   C7    1.4806  119.3801  158.9072  120.8169  1.3924
IC C2   N1   C17  C16   1.4806  115.6335  174.5031  112.7254  1.5245
IC C2   N1   C17  H35   1.4806  115.6335   54.5190  108.8323  1.0995
IC C2   N1   C17  H36   1.4806  115.6335  -62.2515  108.9695  1.0954
IC N1   C2   C3   C4    1.4806  108.2697  -57.1079  111.0457  1.5187
IC N1   C2   C3   H25   1.4806  108.2697   64.1335  108.0549  1.0960
IC N1   C2   C3   H26   1.4806  108.2697 -178.9383  108.7188  1.0940
IC C2   C3   C4   C5    1.5375  111.0457   39.2389  113.5468  1.5161
IC C2   C3   C4   H27   1.5375  111.0457  -80.9928  110.1638  1.0985
IC C2   C3   C4   H28   1.5375  111.0457  160.5459  110.3298  1.0961
IC C3   C4   C5   C6    1.5187  113.5468  -10.4537  122.1896  1.3867
IC C3   C4   C5   C10   1.5187  113.5468  169.7630  117.5892  1.4086
IC N1   C6   C5   C4    1.3920  119.5837   -0.2547  122.1896  1.5161
IC C4   C5   C10  C9    1.5161  117.5892  179.7260  121.0217  1.3839
IC C4   C5   C10  H29   1.5161  117.5892   -0.1511  115.8608  1.0763
IC N1   C6   C7   C8    1.3920  120.8169 -179.2604  119.4399  1.4007
IC N1   C6   C7   C15   1.3920  120.8169    0.3172  120.9138  1.5056
IC C6   C7   C8   C9    1.3924  119.4399   -0.4707  121.7214  1.3971
IC C6   C7   C8   O11   1.3924  119.4399  179.1014  118.5808  1.3575
IC C6   C7   C15  C16   1.3924  120.9138   25.3954  111.8223  1.5375
IC C6   C7   C15  H31   1.3924  120.9138  -96.8956  109.3651  1.0942
IC C6   C7   C15  H32   1.3924  120.9138  144.0121  112.0035  1.0968
IC C7   C8   C9   C10   1.4007  121.7214    0.2849  117.9962  1.3839
IC C7   C8   C9   C14   1.4007  121.7214 -179.8160  119.8282  1.4578
IC C7   C8   O11  C12   1.4007  118.5808 -179.1605  122.5352  1.3448
IC C5   C10  C9   C8    1.4086  121.0217   -0.0174  117.9962  1.3971
IC C8   C9   C14  C13   1.3971  119.8282   -0.8183  118.0830  1.3507
IC C8   C9   C14  C19   1.3971  119.8282  179.0570  123.3163  1.4989
IC C8   O11  C12  C13   1.3575  122.5352   -1.2053  119.3336  1.4514
IC C8   O11  C12  O18   1.3575  122.5352  178.8801  119.4809  1.2214
IC O11  C12  C13  C14   1.3448  119.3336    0.9578  120.5103  1.3507
IC O11  C12  C13  H30   1.3448  119.3336 -178.9461  116.6919  1.0799
IC C9   C14  C13  C12   1.4578  118.0830    0.0412  120.5103  1.4514
IC C9   C14  C19  F20   1.4578  123.3163  -58.0808  109.0871  1.3952
IC C9   C14  C19  F21   1.4578  123.3163 -179.1178  117.8324  1.3694
IC C9   C14  C19  F22   1.4578  123.3163   59.7627  108.8958  1.3945
IC C7   C15  C16  C17   1.5056  111.8223  -49.1523  110.5925  1.5245
IC C7   C15  C16  H33   1.5056  111.8223 -168.6718  108.3476  1.0952
IC C7   C15  C16  H34   1.5056  111.8223   72.9659  110.4359  1.0925
IC N1   C17  C16  C15   1.4692  112.7254   49.3367  110.5925  1.5375


PRES DISU        -0.20  
! This patch is used to provide a disulphide bridge between two CYS residues
GROUP
 ATOM 1CB  CT    -0.10
 ATOM 1SG  ST    -0.00
GROUP
 ATOM 2SG  ST    -0.00
 ATOM 2CB  CT    -0.10
DELETE ATOM 1HG
DELETE ATOM 2HG
BOND 1SG 2SG 
ANGLE  1CB 1SG 2SG      1SG 2SG 2CB    
DIHE   1CA 1CB 1SG 2SG      1HB1 1CB 1SG 2SG      1HB2 1CB 1SG 2SG      
DIHE   1CB 1SG 2SG 2CB    
DIHE   1SG 2SG 2CB 2CA      1SG 2SG 2CB 2HB1     1SG 2SG 2CB 2HB2     
IC     1CA 1CB 1SG 2SG    0.0  0.0  180.0  0.0  0.0
IC     1CB 1SG 2SG 2CB    0.0  0.0  180.0  0.0  0.0
IC     1SG 2SG 2CB 2CA    0.0  0.0  180.0  0.0  0.0

END


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