gro, added example files

examples/1crn.gro

@@ -0,0 +1,330 @@
+CRAMBIN
+  327
+    1THR      N    1   1.705   1.410   0.363
+    1THR     CA    2   1.697   1.278   0.434
+    1THR      C    3   1.569   1.276   0.513
+    1THR      O    4   1.527   1.383   0.559
+    1THR     CB    5   1.817   1.270   0.534
+    1THR    OG1    6   1.933   1.283   0.446
+    1THR    CG2    7   1.815   1.155   0.630
+    2THR      N    8   1.512   1.156   0.526
+    2THR     CA    9   1.386   1.147   0.607
+    2THR      C   10   1.416   1.079   0.738
+    2THR      O   11   1.499   0.986   0.744
+    2THR     CB   12   1.273   1.071   0.526
+    2THR    OG1   13   1.331   0.944   0.493
+    2THR    CG2   14   1.248   1.144   0.389
+    3CYS      N   15   1.349   1.124   0.842
+    3CYS     CA   16   1.366   1.071   0.979
+    3CYS      C   17   1.227   1.043   1.032
+    3CYS      O   18   1.139   1.131   1.018
+    3CYS     CB   19   1.437   1.175   1.069
+    3CYS     SG   20   1.589   1.243   1.002
+    4CYS      N   21   1.202   0.927   1.093
+    4CYS     CA   22   1.065   0.899   1.141
+    4CYS      C   23   1.065   0.879   1.292
+    4CYS      O   24   1.166   0.830   1.349
+    4CYS     CB   25   1.006   0.775   1.068
+    4CYS     SG   26   0.984   0.802   0.890
+    5PRO      N   27   0.956   0.911   1.356
+    5PRO     CA   28   0.945   0.903   1.501
+    5PRO      C   29   0.929   0.767   1.561
+    5PRO      O   30   0.949   0.752   1.682
+    5PRO     CB   31   0.823   0.996   1.535
+    5PRO     CG   32   0.734   0.979   1.411
+    5PRO     CD   33   0.837   0.980   1.296
+    6SER      N   34   0.887   0.669   1.480
+    6SER     CA   35   0.867   0.531   1.528
+    6SER      C   36   0.875   0.438   1.408
+    6SER      O   37   0.873   0.486   1.292
+    6SER     CB   38   0.734   0.512   1.600
+    6SER     OG   39   0.627   0.522   1.503
+    7ILE      N   40   0.888   0.308   1.436
+    7ILE     CA   41   0.891   0.208   1.326
+    7ILE      C   42   0.758   0.209   1.251
+    7ILE      O   43   0.767   0.203   1.125
+    7ILE     CB   44   0.921   0.068   1.392
+    7ILE    CG1   45   1.071   0.070   1.431
+    7ILE    CG2   46   0.881  -0.048   1.297
+    7ILE    CD1   47   1.118  -0.052   1.514
+    8VAL      N   48   0.646   0.216   1.316
+    8VAL     CA   49   0.515   0.221   1.245
+    8VAL      C   50   0.512   0.338   1.146
+    8VAL      O   51   0.466   0.327   1.034
+    8VAL     CB   52   0.400   0.235   1.348
+    8VAL    CG1   53   0.272   0.289   1.287
+    8VAL    CG2   54   0.376   0.103   1.421
+    9ALA      N   55   0.561   0.455   1.194
+    9ALA     CA   56   0.560   0.577   1.108
+    9ALA      C   57   0.644   0.553   0.985
+    9ALA      O   58   0.605   0.593   0.874
+    9ALA     CB   59   0.602   0.698   1.189
+   10ARG      N   60   0.765   0.491   1.000
+   10ARG     CA   61   0.850   0.461   0.884
+   10ARG      C   62   0.780   0.361   0.788
+   10ARG      O   63   0.788   0.378   0.665
+   10ARG     CB   64   0.985   0.402   0.930
+   10ARG     CG   65   1.075   0.361   0.815
+   10ARG     CD   66   1.123   0.470   0.724
+   10ARG     NE   67   1.214   0.557   0.803
+   10ARG     CZ   68   1.276   0.661   0.744
+   10ARG    NH1   69   1.254   0.693   0.616
+   10ARG    NH2   70   1.360   0.732   0.820
+   11SER      N   71   0.719   0.258   0.845
+   11SER     CA   72   0.650   0.158   0.757
+   11SER      C   73   0.538   0.231   0.677
+   11SER      O   74   0.521   0.202   0.556
+   11SER     CB   75   0.591   0.046   0.840
+   11SER     OG   76   0.699  -0.027   0.901
+   12ASN      N   77   0.465   0.318   0.745
+   12ASN     CA   78   0.354   0.394   0.675
+   12ASN      C   79   0.411   0.485   0.569
+   12ASN      O   80   0.354   0.500   0.462
+   12ASN     CB   81   0.266   0.468   0.775
+   12ASN     CG   82   0.180   0.373   0.861
+   12ASN    OD1   83   0.157   0.261   0.817
+   12ASN    ND2   84   0.139   0.425   0.977
+   13PHE      N   85   0.526   0.550   0.600
+   13PHE     CA   86   0.593   0.636   0.506
+   13PHE      C   87   0.630   0.558   0.380
+   13PHE      O   88   0.614   0.607   0.265
+   13PHE     CB   89   0.718   0.699   0.575
+   13PHE     CG   90   0.788   0.801   0.488
+   13PHE    CD1   91   0.891   0.759   0.403
+   13PHE    CD2   92   0.753   0.937   0.498
+   13PHE    CE1   93   0.956   0.854   0.319
+   13PHE    CE2   94   0.818   1.028   0.414
+   13PHE     CZ   95   0.914   0.984   0.329
+   14ASN      N   96   0.690   0.439   0.399
+   14ASN     CA   97   0.733   0.361   0.279
+   14ASN      C   98   0.612   0.321   0.191
+   14ASN      O   99   0.624   0.314   0.068
+   14ASN     CB  100   0.814   0.240   0.324
+   14ASN     CG  101   0.956   0.286   0.373
+   14ASN    OD1  102   1.001   0.389   0.332
+   14ASN    ND2  103   1.012   0.196   0.454
+   15VAL      N  104   0.499   0.293   0.257
+   15VAL     CA  105   0.378   0.260   0.174
+   15VAL      C  106   0.330   0.387   0.100
+   15VAL      O  107   0.295   0.382  -0.019
+   15VAL     CB  108   0.270   0.195   0.261
+   15VAL    CG1  109   0.138   0.183   0.181
+   15VAL    CG2  110   0.317   0.053   0.301
+   16CYS      N  111   0.332   0.499   0.172
+   16CYS     CA  112   0.289   0.628   0.113
+   16CYS      C  113   0.369   0.660  -0.011
+   16CYS      O  114   0.320   0.715  -0.110
+   16CYS     CB  115   0.304   0.737   0.224
+   16CYS     SG  116   0.256   0.901   0.165
+   17ARG      N  117   0.500   0.623  -0.010
+   17ARG     CA  118   0.590   0.649  -0.121
+   17ARG      C  119   0.574   0.556  -0.241
+   17ARG      O  120   0.623   0.590  -0.351
+   17ARG     CB  121   0.737   0.651  -0.073
+   17ARG     CG  122   0.772   0.769   0.021
+   17ARG     CD  123   0.795   0.895  -0.062
+   17ARG     NE  124   0.921   0.886  -0.134
+   17ARG     CZ  125   0.954   0.953  -0.243
+   17ARG    NH1  126   0.866   1.035  -0.303
+   17ARG    NH2  127   1.079   0.949  -0.290
+   18LEU      N  128   0.505   0.441  -0.220
+   18LEU     CA  129   0.493   0.343  -0.333
+   18LEU      C  130   0.440   0.401  -0.462
+   18LEU      O  131   0.499   0.375  -0.569
+   18LEU     CB  132   0.420   0.218  -0.286
+   18LEU     CG  133   0.496   0.118  -0.199
+   18LEU    CD1  134   0.391   0.010  -0.163
+   18LEU    CD2  135   0.613   0.061  -0.277
+   19PRO      N  136   0.333   0.479  -0.454
+   19PRO     CA  137   0.279   0.538  -0.580
+   19PRO      C  138   0.357   0.654  -0.632
+   19PRO      O  139   0.326   0.705  -0.742
+   19PRO     CB  140   0.136   0.577  -0.547
+   19PRO     CG  141   0.122   0.569  -0.399
+   19PRO     CD  142   0.242   0.494  -0.341
+   20GLY      N  143   0.456   0.705  -0.556
+   20GLY     CA  144   0.537   0.819  -0.602
+   20GLY      C  145   0.501   0.948  -0.528
+   20GLY      O  146   0.553   1.051  -0.573
+   21THR      N  147   0.418   0.944  -0.426
+   21THR     CA  148   0.377   1.061  -0.351
+   21THR      C  149   0.502   1.140  -0.304
+   21THR      O  150   0.595   1.076  -0.252
+   21THR     CB  151   0.299   1.019  -0.222
+   21THR    OG1  152   0.205   0.914  -0.262
+   21THR    CG2  153   0.226   1.135  -0.155
+   22PRO      N  154   0.497   1.270  -0.318
+   22PRO     CA  155   0.614   1.351  -0.270
+   22PRO      C  156   0.640   1.323  -0.123
+   22PRO      O  157   0.549   1.306  -0.038
+   22PRO     CB  158   0.570   1.497  -0.292
+   22PRO     CG  159   0.468   1.489  -0.400
+   22PRO     CD  160   0.396   1.357  -0.381
+   23GLU      N  161   0.773   1.330  -0.092
+   23GLU     CA  162   0.811   1.310   0.050
+   23GLU      C  163   0.743   1.407   0.141
+   23GLU      O  164   0.704   1.368   0.254
+   23GLU     CB  165   0.965   1.329   0.066
+   23GLU     CG  166   1.044   1.209   0.006
+   23GLU     CD  167   1.194   1.217   0.039
+   23GLU    OE1  168   1.242   1.322   0.068
+   23GLU    OE2  169   1.254   1.107   0.029
+   24ALA      N  170   0.721   1.533   0.097
+   24ALA     CA  171   0.661   1.632   0.191
+   24ALA      C  172   0.521   1.594   0.235
+   24ALA      O  173   0.478   1.617   0.350
+   24ALA     CB  174   0.660   1.770   0.125
+   25ILE      N  175   0.444   1.532   0.140
+   25ILE     CA  176   0.307   1.489   0.176
+   25ILE      C  177   0.308   1.364   0.264
+   25ILE      O  178   0.231   1.352   0.358
+   25ILE     CB  179   0.220   1.464   0.046
+   25ILE    CG1  180   0.182   1.605  -0.013
+   25ILE    CG2  181   0.090   1.386   0.081
+   25ILE    CD1  182   0.076   1.676   0.076
+   26CYS      N  183   0.403   1.276   0.231
+   26CYS     CA  184   0.418   1.155   0.319
+   26CYS      C  185   0.463   1.194   0.460
+   26CYS      O  186   0.423   1.125   0.555
+   26CYS     CB  187   0.504   1.052   0.254
+   26CYS     SG  188   0.435   0.979   0.102
+   27ALA      N  189   0.541   1.301   0.469
+   27ALA     CA  190   0.588   1.350   0.603
+   27ALA      C  191   0.470   1.391   0.688
+   27ALA      O  192   0.453   1.342   0.803
+   27ALA     CB  193   0.688   1.462   0.583
+   28THR      N  194   0.383   1.480   0.636
+   28THR     CA  195   0.269   1.522   0.719
+   28THR      C  196   0.167   1.413   0.743
+   28THR      O  197   0.095   1.411   0.847
+   28THR     CB  198   0.199   1.652   0.661
+   28THR    OG1  199   0.166   1.622   0.523
+   28THR    CG2  200   0.291   1.774   0.670
+   29TYR      N  201   0.162   1.319   0.651
+   29TYR     CA  202   0.072   1.204   0.666
+   29TYR      C  203   0.112   1.112   0.781
+   29TYR      O  204   0.029   1.063   0.854
+   29TYR     CB  205   0.075   1.123   0.532
+   29TYR     CG  206  -0.020   1.004   0.535
+   29TYR    CD1  207  -0.155   1.034   0.564
+   29TYR    CD2  208   0.019   0.875   0.510
+   29TYR    CE1  209  -0.250   0.933   0.567
+   29TYR    CE2  210  -0.080   0.771   0.516
+   29TYR     CZ  211  -0.208   0.803   0.543
+   29TYR     OH  212  -0.310   0.706   0.546
+   30THR      N  213   0.247   1.098   0.799
+   30THR     CA  214   0.299   0.999   0.895
+   30THR      C  215   0.361   1.051   1.023
+   30THR      O  216   0.377   0.971   1.119
+   30THR     CB  217   0.408   0.910   0.822
+   30THR    OG1  218   0.512   1.003   0.782
+   30THR    CG2  219   0.349   0.832   0.703
+   31GLY      N  220   0.398   1.176   1.024
+   31GLY     CA  221   0.477   1.234   1.136
+   31GLY      C  222   0.626   1.224   1.111
+   31GLY      O  223   0.704   1.275   1.195
+   32CYS      N  224   0.671   1.163   0.999
+   32CYS     CA  225   0.814   1.169   0.964
+   32CYS      C  226   0.850   1.314   0.921
+   32CYS      O  227   0.758   1.395   0.894
+   32CYS     CB  228   0.850   1.069   0.853
+   32CYS     SG  229   0.805   0.899   0.888
+   33ILE      N  230   0.979   1.341   0.917
+   33ILE     CA  231   1.028   1.476   0.882
+   33ILE      C  232   1.135   1.466   0.774
+   33ILE      O  233   1.197   1.358   0.755
+   33ILE     CB  234   1.079   1.554   1.008
+   33ILE    CG1  235   1.206   1.480   1.067
+   33ILE    CG2  236   0.968   1.569   1.114
+   33ILE    CD1  237   1.273   1.568   1.178
+   34ILE      N  238   1.149   1.577   0.704
+   34ILE     CA  239   1.255   1.588   0.604
+   34ILE      C  240   1.359   1.692   0.656
+   34ILE      O  241   1.317   1.801   0.695
+   34ILE     CB  242   1.199   1.636   0.468
+   34ILE    CG1  243   1.091   1.534   0.416
+   34ILE    CG2  244   1.313   1.652   0.363
+   34ILE    CD1  245   1.015   1.602   0.294
+   35ILE      N  246   1.486   1.649   0.654
+   35ILE     CA  247   1.593   1.745   0.694
+   35ILE      C  248   1.691   1.755   0.582
+   35ILE      O  249   1.710   1.666   0.497
+   35ILE     CB  250   1.662   1.699   0.828
+   35ILE    CG1  251   1.736   1.565   0.807
+   35ILE    CG2  252   1.559   1.697   0.943
+   35ILE    CD1  253   1.830   1.521   0.922
+   36PRO      N  254   1.766   1.867   0.581
+   36PRO     CA  255   1.863   1.886   0.474
+   36PRO      C  256   1.992   1.804   0.495
+   36PRO      O  257   2.059   1.774   0.394
+   36PRO     CB  258   1.895   2.036   0.478
+   36PRO     CG  259   1.824   2.094   0.591
+   36PRO     CD  260   1.737   1.990   0.660
+   37GLY      N  261   2.017   1.773   0.622
+   37GLY     CA  262   2.145   1.697   0.651
+   37GLY      C  263   2.114   1.548   0.643
+   37GLY      O  264   2.014   1.502   0.588
+   38ALA      N  265   2.205   1.470   0.703
+   38ALA     CA  266   2.202   1.324   0.702
+   38ALA      C  267   2.194   1.263   0.840
+   38ALA      O  268   2.187   1.139   0.844
+   38ALA     CB  269   2.325   1.270   0.627
+   39THR      N  270   2.189   1.344   0.944
+   39THR     CA  271   2.194   1.291   1.081
+   39THR      C  272   2.062   1.319   1.152
+   39THR      O  273   2.036   1.432   1.195
+   39THR     CB  274   2.313   1.360   1.159
+   39THR    OG1  275   2.428   1.340   1.071
+   39THR    CG2  276   2.334   1.293   1.296
+   40CYS      N  277   1.983   1.211   1.164
+   40CYS     CA  278   1.850   1.231   1.230
+   40CYS      C  279   1.868   1.245   1.378
+   40CYS      O  280   1.953   1.172   1.436
+   40CYS     CB  281   1.758   1.112   1.200
+   40CYS     SG  282   1.720   1.093   1.024
+   41PRO      N  283   1.788   1.327   1.443
+   41PRO     CA  284   1.792   1.342   1.588
+   41PRO      C  285   1.739   1.221   1.659
+   41PRO      O  286   1.665   1.137   1.603
+   41PRO     CB  287   1.708   1.466   1.615
+   41PRO     CG  288   1.610   1.469   1.500
+   41PRO     CD  289   1.686   1.415   1.378
+   42GLY      N  290   1.773   1.212   1.788
+   42GLY     CA  291   1.733   1.096   1.869
+   42GLY      C  292   1.587   1.069   1.887
+   42GLY      O  293   1.543   0.955   1.917
+   43ASP      N  294   1.504   1.175   1.872
+   43ASP     CA  295   1.356   1.157   1.884
+   43ASP      C  296   1.294   1.123   1.747
+   43ASP      O  297   1.172   1.104   1.743
+   43ASP     CB  298   1.293   1.274   1.958
+   43ASP     CG  299   1.314   1.409   1.896
+   43ASP    OD1  300   1.411   1.430   1.821
+   43ASP    OD2  301   1.227   1.496   1.926
+   44TYR      N  302   1.372   1.117   1.643
+   44TYR     CA  303   1.326   1.074   1.508
+   44TYR      C  304   1.428   0.969   1.461
+   44TYR      O  305   1.493   0.986   1.357
+   44TYR     CB  306   1.320   1.191   1.407
+   44TYR     CG  307   1.200   1.282   1.440
+   44TYR    CD1  308   1.212   1.385   1.533
+   44TYR    CD2  309   1.077   1.262   1.376
+   44TYR    CE1  310   1.105   1.467   1.561
+   44TYR    CE2  311   0.968   1.343   1.405
+   44TYR     CZ  312   0.980   1.446   1.500
+   44TYR     OH  313   0.874   1.526   1.527
+   45ALA      N  314   1.434   0.864   1.542
+   45ALA     CA  315   1.544   0.767   1.525
+   45ALA      C  316   1.517   0.653   1.428
+   45ALA      O  317   1.609   0.571   1.404
+   45ALA     CB  318   1.568   0.710   1.668
+   46ASN      N  319   1.397   0.650   1.374
+   46ASN     CA  320   1.351   0.539   1.288
+   46ASN      C  321   1.331   0.585   1.145
+   46ASN      O  322   1.373   0.693   1.103
+   46ASN     CB  323   1.227   0.477   1.350
+   46ASN     CG  324   1.254   0.430   1.492
+   46ASN    OD1  325   1.198   0.485   1.589
+   46ASN    ND2  326   1.341   0.330   1.502
+   46ASN    OXT  327   1.270   0.497   1.075
+   4.09600   1.86500   2.25180   0.00000   0.00000   0.00000   0.00000  -0.03026   0.00000

examples/test.gro

@@ -0,0 +1,9 @@
+MD of 2 waters, t= 4.2
+    6
+    1WATER  OW1    1   0.126   1.624   1.679  0.1227 -0.0580  0.0434
+    1WATER  HW2    2   0.190   1.661   1.747  0.8085  0.3191 -0.7791
+    1WATER  HW3    3   0.177   1.568   1.613 -0.9045 -2.6469  1.3180
+    2WATER  OW1    4   1.275   0.053   0.622  0.2519  0.3140 -0.1734
+    2WATER  HW2    5   1.337   0.002   0.680 -1.0641 -1.1349  0.0257
+    2WATER  HW3    6   1.326   0.120   0.568  1.9427 -0.8216 -0.0244
+   1.82060   1.82060   1.82060