[gmx-users] about the topology file

Xiangyang Liu shangdongliu at gmail.com
Thu Nov 2 12:32:13 CET 2006


hello Tsjerk:
Thank you very much! That does work, but another problem appeared as
following:
creating statusfile for 1 node...
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 1284 of the 1485 non-bonded parameter combinations
WARNING 1 [file "com.top", line 519]:
  Too few parameters on line (source file toppush.c, line 932)
WARNING 2 [file "com.top", line 520]:
  Too few parameters on line (source file toppush.c, line 932)
processing coordinates...
Fatal error: number of coordinates in coordinate file (com_wat.gro, 2837)
             does not match topology (com.top, 0)
actually i only perform the following:

editconf ¨Cbt cubic ¨Cf com.gro ¨Co com_box.gro ¨Cd 0.8

genbox ¨Ccp com_box.gro ¨Ccs spc216.gro  ¨Cp com.top ¨Co com_wat.gro

grompp ¨Cf em.mdp ¨Cc com_wat.gro ¨Cp com.top ¨Co com_em.tpr

and my com.gro file was as following:

PRODRG COORDS
   80
    1DRG  CAH      1  -0.832  -0.624  -0.960
    1DRG  CAS      2  -0.746  -0.538  -0.867
    1DRG  CAT      3  -0.710  -0.410  -0.942
    1DRG  CBI      4  -0.621  -0.618  -0.830
    1DRG  CCF      5  -0.555  -0.585  -0.694
    1DRG  CCG      6  -0.647  -0.615  -0.575
    1DRG  OCU      7  -0.750  -0.706  -0.587
    1DRG  OBJ      8  -0.629  -0.560  -0.467
    1DRG  NCE      9  -0.506  -0.445  -0.688
    1DRG  HAG     10  -0.556  -0.385  -0.626
    1DRG  CCD     11  -0.401  -0.405  -0.761
    1DRG  OBH     12  -0.345  -0.480  -0.843
    1DRG  CCC     13  -0.347  -0.263  -0.745
    1DRG  CBG     14  -0.439  -0.163  -0.817
    1DRG  CAQ     15  -0.381  -0.024  -0.851
    1DRG  CAG     16  -0.248  -0.030  -0.926
    1DRG  CAR     17  -0.363   0.065  -0.727
    1DRG  NCB     18  -0.326  -0.229  -0.603
    1DRG  HAF     19  -0.405  -0.241  -0.543
    1DRG  CCA     20  -0.206  -0.185  -0.563
    1DRG  OBF     21  -0.113  -0.159  -0.640
    1DRG  CBZ     22  -0.187  -0.168  -0.413
    1DRG  CBE     23  -0.126  -0.302  -0.370
    1DRG  CAO     24  -0.241  -0.394  -0.332
    1DRG  OAF     25  -0.338  -0.339  -0.274
    1DRG  OAP     26  -0.230  -0.514  -0.360
    1DRG  NBY     27  -0.106  -0.046  -0.388
    1DRG  HAE     28  -0.084   0.000  -0.473
    1DRG  CBX     29  -0.062   0.009  -0.273
    1DRG  OBD     30  -0.012   0.122  -0.272
    1DRG  CBW     31  -0.067  -0.063  -0.137
    1DRG  CBC     32   0.078  -0.071  -0.084
    1DRG  CAN     33   0.164  -0.170  -0.163
    1DRG  CBB     34   0.089  -0.114   0.063
    1DRG  NBV     35  -0.154   0.013  -0.045
    1DRG  HAD     36  -0.131   0.111  -0.043
    1DRG  CBU     37  -0.254  -0.032   0.032
    1DRG  OBA     38  -0.296   0.039   0.123
    1DRG  CBT     39  -0.315  -0.174   0.014
    1DRG  CAZ     40  -0.241  -0.277   0.099
    1DRG  CAL     41  -0.206  -0.403   0.018
    1DRG  CAE     42  -0.326  -0.495  -0.002
    1DRG  CAM     43  -0.094  -0.481   0.088
    1DRG  NBS     44  -0.452  -0.166   0.069
    1DRG  HAC     45  -0.449  -0.181   0.167
    1DRG  CBR     46  -0.575  -0.144   0.017
    1DRG  OAY     47  -0.666  -0.135   0.100
    1DRG  CBQ     48  -0.618  -0.126  -0.131
    1DRG  CAX     49  -0.520  -0.056  -0.228
    1DRG  CAJ     50  -0.533   0.096  -0.242
    1DRG  CAD     51  -0.499   0.173  -0.114
    1DRG  CAK     52  -0.673   0.137  -0.289
    1DRG  NBP     53  -0.666  -0.245  -0.201
    1DRG  HAB     54  -0.595  -0.302  -0.244
    1DRG  C       55  -0.797  -0.274  -0.207
    1DRG  O       56  -0.872  -0.267  -0.109
    1DRG  CA      57  -0.856  -0.322  -0.340
    1DRG  CB      58  -0.777  -0.276  -0.463
    1DRG  CG      59  -0.821  -0.140  -0.516
    1DRG  CD      60  -0.725  -0.105  -0.629
    1DRG  OE2     61  -0.635  -0.023  -0.602
    1DRG  OE1     62  -0.741  -0.164  -0.738
    1DRG  N       63  -0.871  -0.467  -0.358
    1DRG  HAA     64  -0.795  -0.522  -0.325
    1DRG  CBL     65  -0.981  -0.519  -0.414
    1DRG  OAU     66  -1.093  -0.467  -0.410
    1DRG  CBK     67  -0.968  -0.654  -0.484
    1DRG  CCT     68  -0.833  -0.725  -0.469
    1DRG  CCS     69  -0.860  -0.875  -0.449
    1DRG  CCR     70  -0.929  -0.913  -0.316
    1DRG  CCQ     71  -0.842  -0.888  -0.192
    1DRG  CCP     72  -0.880  -0.760  -0.116
    1DRG  CCO     73  -0.763  -0.714  -0.029
    1DRG  CCN     74  -0.792  -0.577   0.034
    1DRG  CCM     75  -0.676  -0.523   0.119
    1DRG  CCL     76  -0.670  -0.578   0.263
    1DRG  CCK     77  -0.593  -0.710   0.282
    1DRG  CCJ     78  -0.440  -0.698   0.279
    1DRG  CCI     79  -0.385  -0.625   0.402
    1DRG  CCH     80  -0.232  -0.622   0.401
   1.51200   1.51200   1.51200
Thank you very much!
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