6/11/2012 by Adam

Yet another revision of xdrf2pdb-m. Error detected in description; directory src-M all pertains to
multi-chain systems (but the programs can also be used for single-chain systems). xdrf2pdb-m for
single-chain systems is in src

diff --git a/bin/xdrf2pdb-m b/bin/xdrf2pdb-m
new file mode 100755 (executable)
index 0000000..201ccb1
Binary files /dev/null and b/bin/xdrf2pdb-m differ

diff --git a/doc/XDRFPDB.TXT b/doc/XDRFPDB.TXT
index 988665f..f266720 100644 (file)
--- a/doc/XDRFPDB.TXT
+++ b/doc/XDRFPDB.TXT
@@ -102,15 +102,20 @@ pdbfile (cxfile with extension changed from cx to pdb) - the output PDB file
 4.2 XDRF2PDB-M
 
 Command line syntax:
-xdrf2pdb-m one/three seqfile cxfile [ntraj] [itraj]
+xdrf2pdb-m xdrf2pdb-m one/three seqfile cxfile ntraj itraj [pdbfile] [freq]
 
 cxfile - the name of the compressed trajectory file from an UNRES/MREMD run
          carried out with TRAJ1FILE (conformations from all trajectories
          output to a single file)
       
-ntraj (1) - number of trajectories in the multi-trajectory run
+ntraj - number of trajectories in the multi-trajectory run
 
-itraj (1) - the number of trajectory to be extracted
+itraj - the number of trajectory to be extracted
+
+pdbfile - (cxfile-without-cx-itraj.pdb) the name of file to write the Cartesian 
+        coordinates of trajectory itraj to
+
+freq (1) - output frequency
 
 The xdrf2pdb program to convert cx files to pdb files
 

diff --git a/examples/unres/MD/ff_1l2y_1le1/MREMD/1L2Y_MREMD_MD000_030.pdb b/examples/unres/MD/ff_1l2y_1le1/MREMD/1L2Y_MREMD_MD000_030.pdb
new file mode 100644 (file)
index 0000000..891974b
--- /dev/null
+++ b/examples/unres/MD/ff_1l2y_1le1/MREMD/1L2Y_MREMD_MD000_030.pdb
@@ -0,0 +1,600 @@
+REMARK Structure    30                                    ENERGY    -2.68397E+01
+ATOM      1  CA  ASN     1       2.648   0.843   1.842
+ATOM      2  CB  ASN     1       3.630   0.680   3.586
+ATOM      3  CA  LEU     2       3.133  -2.912   1.493
+ATOM      4  CB  LEU     2       3.001  -4.566   0.220
+ATOM      5  CA  TYR     3       6.893  -3.188   1.081
+ATOM      6  CB  TYR     3       7.554  -0.438   2.885
+ATOM      7  CA  ILE     4       6.879  -7.033   0.740
+ATOM      8  CB  ILE     4       6.197  -8.647  -0.003
+ATOM      9  CA  GLN     5      10.619  -7.494   0.119
+ATOM     10  CB  GLN     5      10.942  -5.539   1.499
+ATOM     11  CA  TRP     6      10.259 -11.299  -0.163
+ATOM     12  CB  TRP     6       7.686 -13.849  -0.760
+ATOM     13  CA  LEU     7      13.955 -11.645  -0.999
+ATOM     14  CB  LEU     7      14.284  -9.721  -0.262
+ATOM     15  CA  LYS     8      13.933 -15.464  -1.118
+ATOM     16  CB  LYS     8      11.734 -15.142  -2.641
+ATOM     17  CA  ASP     9      17.545 -15.853  -2.380
+ATOM     18  CB  ASP     9      18.425 -14.455  -1.204
+ATOM     19  CA  GLY    10      17.525 -19.685  -2.237
+ATOM     20  CA  GLY    11      21.051 -20.532  -3.460
+ATOM     21  CA  PRO    12      21.733 -24.309  -3.034
+ATOM     22  CB  PRO    12      21.258 -24.316  -4.380
+ATOM     23  CA  SER    13      25.119 -25.103  -1.493
+ATOM     24  CB  SER    13      25.462 -23.872  -1.190
+ATOM     25  CA  SER    14      26.931 -28.125  -0.030
+ATOM     26  CB  SER    14      26.738 -29.260  -0.650
+ATOM     27  CA  GLY    15      30.342 -26.545   0.679
+ATOM     28  CA  ARG    16      32.259 -29.512   2.145
+ATOM     29  CB  ARG    16      30.559 -30.774  -0.540
+ATOM     30  CA  PRO    17      35.966 -29.838   2.917
+ATOM     31  CB  PRO    17      35.455 -30.678   3.941
+ATOM     32  CA  PRO    18      36.981 -30.997  -0.588
+ATOM     33  CB  PRO    18      36.403 -29.749  -0.956
+ATOM     34  CA  PRO    19      40.448 -32.164   0.632
+ATOM     35  CB  PRO    19      39.610 -32.822   1.578
+ATOM     36  CA  SER    20      42.177 -32.871  -2.680
+ATOM     37  CB  SER    20      41.322 -32.231  -3.428
+TER
+CONECT    1    3    2
+CONECT    3    5    4
+CONECT    5    7    6
+CONECT    7    9    8
+CONECT    9   11   10
+CONECT   11   13   12
+CONECT   13   15   14
+CONECT   15   17   16
+CONECT   17   19   18
+CONECT   19   20
+CONECT   20   21
+CONECT   21   23   22
+CONECT   23   25   24
+CONECT   25   27   26
+CONECT   27   28
+CONECT   28   30   29
+CONECT   30   32   31
+CONECT   32   34   33
+CONECT   34   36   35
+CONECT   36   37
+ENDMDL
+REMARK Structure    62                                    ENERGY    -2.69690E+01
+ATOM      1  CA  ASN     1       2.024   0.037   1.808
+ATOM      2  CB  ASN     1       3.063  -0.005   3.525
+ATOM      3  CA  LEU     2       2.451  -3.722   1.657
+ATOM      4  CB  LEU     2       2.136  -5.497   0.619
+ATOM      5  CA  TYR     3       6.144  -3.994   0.840
+ATOM      6  CB  TYR     3       6.912  -1.132   2.407
+ATOM      7  CA  ILE     4       6.177  -7.840   0.818
+ATOM      8  CB  ILE     4       5.431  -9.519   0.306
+ATOM      9  CA  GLN     5       9.890  -8.066  -0.093
+ATOM     10  CB  GLN     5      10.157  -5.870   0.906
+ATOM     11  CA  TRP     6       9.808 -11.907   0.011
+ATOM     12  CB  TRP     6       7.177 -14.456  -0.303
+ATOM     13  CA  LEU     7      13.462 -11.995  -1.072
+ATOM     14  CB  LEU     7      13.664 -10.016  -0.447
+ATOM     15  CA  LYS     8      13.709 -15.836  -0.936
+ATOM     16  CB  LYS     8      11.366 -15.809  -2.295
+ATOM     17  CA  ASP     9      17.302 -15.987  -2.273
+ATOM     18  CB  ASP     9      18.112 -14.415  -1.283
+ATOM     19  CA  GLY    10      17.590 -19.804  -1.955
+ATOM     20  CA  GLY    11      21.116 -20.537  -3.228
+ATOM     21  CA  PRO    12      22.010 -24.247  -2.638
+ATOM     22  CB  PRO    12      21.418 -24.363  -3.927
+ATOM     23  CA  SER    13      25.520 -24.814  -1.300
+ATOM     24  CB  SER    13      25.805 -23.544  -1.147
+ATOM     25  CA  SER    14      27.619 -27.552   0.321
+ATOM     26  CB  SER    14      27.380 -28.758  -0.125
+ATOM     27  CA  GLY    15      31.036 -25.818   0.548
+ATOM     28  CA  ARG    16      33.269 -28.529   2.061
+ATOM     29  CB  ARG    16      31.256 -30.276  -0.086
+ATOM     30  CA  PRO    17      37.041 -28.667   2.524
+ATOM     31  CB  PRO    17      36.621 -29.338   3.706
+ATOM     32  CA  PRO    18      37.821 -29.972  -1.002
+ATOM     33  CB  PRO    18      37.209 -28.749  -1.392
+ATOM     34  CA  PRO    19      41.389 -31.030   0.040
+ATOM     35  CB  PRO    19      40.651 -31.600   1.112
+ATOM     36  CA  SER    20      42.888 -31.914  -3.343
+ATOM     37  CB  SER    20      42.004 -31.453  -4.192
+TER
+CONECT    1    3    2
+CONECT    3    5    4
+CONECT    5    7    6
+CONECT    7    9    8
+CONECT    9   11   10
+CONECT   11   13   12
+CONECT   13   15   14
+CONECT   15   17   16
+CONECT   17   19   18
+CONECT   19   20
+CONECT   20   21
+CONECT   21   23   22
+CONECT   23   25   24
+CONECT   25   27   26
+CONECT   27   28
+CONECT   28   30   29
+CONECT   30   32   31
+CONECT   32   34   33
+CONECT   34   36   35
+CONECT   36   37
+ENDMDL
+REMARK Structure    94                                    ENERGY    -2.72182E+01
+ATOM      1  CA  ASN     1       1.912  -0.027   1.807
+ATOM      2  CB  ASN     1       2.942  -0.038   3.530
+ATOM      3  CA  LEU     2       2.400  -3.792   1.693
+ATOM      4  CB  LEU     2       2.191  -5.513   0.541
+ATOM      5  CA  TYR     3       6.105  -4.046   0.908
+ATOM      6  CB  TYR     3       6.758  -1.117   2.406
+ATOM      7  CA  ILE     4       6.246  -7.877   0.875
+ATOM      8  CB  ILE     4       5.460  -9.536   0.357
+ATOM      9  CA  GLN     5       9.950  -8.096  -0.071
+ATOM     10  CB  GLN     5      10.265  -5.871   0.828
+ATOM     11  CA  TRP     6       9.933 -11.932   0.021
+ATOM     12  CB  TRP     6       7.214 -14.396  -0.216
+ATOM     13  CA  LEU     7      13.568 -12.090  -1.102
+ATOM     14  CB  LEU     7      13.834 -10.100  -0.536
+ATOM     15  CA  LYS     8      13.760 -15.921  -0.926
+ATOM     16  CB  LYS     8      11.393 -15.774  -2.226
+ATOM     17  CA  ASP     9      17.328 -16.109  -2.328
+ATOM     18  CB  ASP     9      18.188 -14.567  -1.326
+ATOM     19  CA  GLY    10      17.545 -19.923  -1.966
+ATOM     20  CA  GLY    11      21.077 -20.611  -3.286
+ATOM     21  CA  PRO    12      22.021 -24.302  -2.679
+ATOM     22  CB  PRO    12      21.456 -24.434  -3.977
+ATOM     23  CA  SER    13      25.540 -24.776  -1.316
+ATOM     24  CB  SER    13      25.781 -23.505  -1.114
+ATOM     25  CA  SER    14      27.608 -27.564   0.264
+ATOM     26  CB  SER    14      27.404 -28.738  -0.279
+ATOM     27  CA  GLY    15      31.012 -25.836   0.597
+ATOM     28  CA  ARG    16      33.193 -28.580   2.119
+ATOM     29  CB  ARG    16      31.210 -30.297  -0.084
+ATOM     30  CA  PRO    17      36.972 -28.611   2.581
+ATOM     31  CB  PRO    17      36.591 -29.288   3.774
+ATOM     32  CA  PRO    18      37.746 -29.934  -0.948
+ATOM     33  CB  PRO    18      37.054 -28.753  -1.339
+ATOM     34  CA  PRO    19      41.390 -30.809  -0.010
+ATOM     35  CB  PRO    19      40.703 -31.432   1.068
+ATOM     36  CA  SER    20      42.897 -31.637  -3.403
+ATOM     37  CB  SER    20      42.032 -31.059  -4.201
+TER
+CONECT    1    3    2
+CONECT    3    5    4
+CONECT    5    7    6
+CONECT    7    9    8
+CONECT    9   11   10
+CONECT   11   13   12
+CONECT   13   15   14
+CONECT   15   17   16
+CONECT   17   19   18
+CONECT   19   20
+CONECT   20   21
+CONECT   21   23   22
+CONECT   23   25   24
+CONECT   25   27   26
+CONECT   27   28
+CONECT   28   30   29
+CONECT   30   32   31
+CONECT   32   34   33
+CONECT   34   36   35
+CONECT   36   37
+ENDMDL
+REMARK Structure   126                                    ENERGY    -2.72196E+01
+ATOM      1  CA  ASN     1       1.915  -0.044   1.807
+ATOM      2  CB  ASN     1       2.946  -0.054   3.530
+ATOM      3  CA  LEU     2       2.403  -3.809   1.696
+ATOM      4  CB  LEU     2       2.193  -5.531   0.545
+ATOM      5  CA  TYR     3       6.107  -4.064   0.908
+ATOM      6  CB  TYR     3       6.761  -1.134   2.403
+ATOM      7  CA  ILE     4       6.248  -7.896   0.877
+ATOM      8  CB  ILE     4       5.461  -9.554   0.361
+ATOM      9  CA  GLN     5       9.951  -8.118  -0.072
+ATOM     10  CB  GLN     5      10.268  -5.892   0.826
+ATOM     11  CA  TRP     6       9.930 -11.953   0.023
+ATOM     12  CB  TRP     6       7.210 -14.418  -0.207
+ATOM     13  CA  LEU     7      13.563 -12.116  -1.104
+ATOM     14  CB  LEU     7      13.832 -10.127  -0.539
+ATOM     15  CA  LYS     8      13.749 -15.948  -0.926
+ATOM     16  CB  LYS     8      11.381 -15.797  -2.224
+ATOM     17  CA  ASP     9      17.316 -16.142  -2.330
+ATOM     18  CB  ASP     9      18.181 -14.604  -1.328
+ATOM     19  CA  GLY    10      17.526 -19.957  -1.967
+ATOM     20  CA  GLY    11      21.058 -20.648  -3.288
+ATOM     21  CA  PRO    12      22.003 -24.339  -2.683
+ATOM     22  CB  PRO    12      21.438 -24.471  -3.981
+ATOM     23  CA  SER    13      25.521 -24.806  -1.317
+ATOM     24  CB  SER    13      25.759 -23.534  -1.115
+ATOM     25  CA  SER    14      27.602 -27.583   0.264
+ATOM     26  CB  SER    14      27.404 -28.758  -0.280
+ATOM     27  CA  GLY    15      30.994 -25.833   0.600
+ATOM     28  CA  ARG    16      33.196 -28.561   2.120
+ATOM     29  CB  ARG    16      31.220 -30.295  -0.075
+ATOM     30  CA  PRO    17      36.975 -28.551   2.581
+ATOM     31  CB  PRO    17      36.603 -29.235   3.772
+ATOM     32  CA  PRO    18      37.763 -29.857  -0.951
+ATOM     33  CB  PRO    18      37.058 -28.682  -1.339
+ATOM     34  CA  PRO    19      41.417 -30.693  -0.018
+ATOM     35  CB  PRO    19      40.738 -31.326   1.059
+ATOM     36  CA  SER    20      42.933 -31.494  -3.413
+ATOM     37  CB  SER    20      42.068 -30.914  -4.207
+TER
+CONECT    1    3    2
+CONECT    3    5    4
+CONECT    5    7    6
+CONECT    7    9    8
+CONECT    9   11   10
+CONECT   11   13   12
+CONECT   13   15   14
+CONECT   15   17   16
+CONECT   17   19   18
+CONECT   19   20
+CONECT   20   21
+CONECT   21   23   22
+CONECT   23   25   24
+CONECT   25   27   26
+CONECT   27   28
+CONECT   28   30   29
+CONECT   30   32   31
+CONECT   32   34   33
+CONECT   34   36   35
+CONECT   36   37
+ENDMDL
+REMARK Structure   158                                    ENERGY    -2.72206E+01
+ATOM      1  CA  ASN     1       1.916  -0.060   1.807
+ATOM      2  CB  ASN     1       2.948  -0.068   3.529
+ATOM      3  CA  LEU     2       2.402  -3.825   1.698
+ATOM      4  CB  LEU     2       2.190  -5.548   0.549
+ATOM      5  CA  TYR     3       6.105  -4.083   0.907
+ATOM      6  CB  TYR     3       6.762  -1.153   2.400
+ATOM      7  CA  ILE     4       6.243  -7.915   0.879
+ATOM      8  CB  ILE     4       5.455  -9.573   0.365
+ATOM      9  CA  GLN     5       9.945  -8.141  -0.074
+ATOM     10  CB  GLN     5      10.265  -5.915   0.824
+ATOM     11  CA  TRP     6       9.920 -11.977   0.025
+ATOM     12  CB  TRP     6       7.199 -14.440  -0.201
+ATOM     13  CA  LEU     7      13.552 -12.144  -1.104
+ATOM     14  CB  LEU     7      13.823 -10.154  -0.541
+ATOM     15  CA  LYS     8      13.735 -15.975  -0.923
+ATOM     16  CB  LYS     8      11.367 -15.824  -2.220
+ATOM     17  CA  ASP     9      17.301 -16.173  -2.330
+ATOM     18  CB  ASP     9      18.166 -14.632  -1.330
+ATOM     19  CA  GLY    10      17.511 -19.987  -1.964
+ATOM     20  CA  GLY    11      21.042 -20.677  -3.287
+ATOM     21  CA  PRO    12      21.992 -24.366  -2.680
+ATOM     22  CB  PRO    12      21.427 -24.500  -3.978
+ATOM     23  CA  SER    13      25.512 -24.823  -1.315
+ATOM     24  CB  SER    13      25.746 -23.549  -1.115
+ATOM     25  CA  SER    14      27.606 -27.588   0.268
+ATOM     26  CB  SER    14      27.413 -28.765  -0.275
+ATOM     27  CA  GLY    15      30.989 -25.819   0.599
+ATOM     28  CA  ARG    16      33.209 -28.533   2.120
+ATOM     29  CB  ARG    16      31.238 -30.283  -0.067
+ATOM     30  CA  PRO    17      36.988 -28.493   2.577
+ATOM     31  CB  PRO    17      36.623 -29.180   3.768
+ATOM     32  CA  PRO    18      37.783 -29.792  -0.957
+ATOM     33  CB  PRO    18      37.067 -28.623  -1.344
+ATOM     34  CA  PRO    19      41.445 -30.600  -0.028
+ATOM     35  CB  PRO    19      40.771 -31.239   1.049
+ATOM     36  CA  SER    20      42.965 -31.388  -3.425
+ATOM     37  CB  SER    20      42.099 -30.806  -4.218
+TER
+CONECT    1    3    2
+CONECT    3    5    4
+CONECT    5    7    6
+CONECT    7    9    8
+CONECT    9   11   10
+CONECT   11   13   12
+CONECT   13   15   14
+CONECT   15   17   16
+CONECT   17   19   18
+CONECT   19   20
+CONECT   20   21
+CONECT   21   23   22
+CONECT   23   25   24
+CONECT   25   27   26
+CONECT   27   28
+CONECT   28   30   29
+CONECT   30   32   31
+CONECT   32   34   33
+CONECT   34   36   35
+CONECT   36   37
+ENDMDL
+REMARK Structure   190                                    ENERGY    -2.72215E+01
+ATOM      1  CA  ASN     1       1.911  -0.077   1.804
+ATOM      2  CB  ASN     1       2.945  -0.084   3.525
+ATOM      3  CA  LEU     2       2.396  -3.842   1.699
+ATOM      4  CB  LEU     2       2.182  -5.567   0.553
+ATOM      5  CA  TYR     3       6.098  -4.103   0.905
+ATOM      6  CB  TYR     3       6.757  -1.171   2.395
+ATOM      7  CA  ILE     4       6.235  -7.935   0.882
+ATOM      8  CB  ILE     4       5.445  -9.594   0.370
+ATOM      9  CA  GLN     5       9.936  -8.164  -0.075
+ATOM     10  CB  GLN     5      10.257  -5.938   0.820
+ATOM     11  CA  TRP     6       9.909 -12.000   0.029
+ATOM     12  CB  TRP     6       7.187 -14.462  -0.192
+ATOM     13  CA  LEU     7      13.539 -12.169  -1.104
+ATOM     14  CB  LEU     7      13.811 -10.179  -0.544
+ATOM     15  CA  LYS     8      13.722 -16.001  -0.918
+ATOM     16  CB  LYS     8      11.352 -15.851  -2.213
+ATOM     17  CA  ASP     9      17.286 -16.199  -2.328
+ATOM     18  CB  ASP     9      18.151 -14.656  -1.333
+ATOM     19  CA  GLY    10      17.499 -20.012  -1.958
+ATOM     20  CA  GLY    11      21.029 -20.701  -3.284
+ATOM     21  CA  PRO    12      21.986 -24.387  -2.675
+ATOM     22  CB  PRO    12      21.420 -24.523  -3.972
+ATOM     23  CA  SER    13      25.508 -24.832  -1.313
+ATOM     24  CB  SER    13      25.739 -23.558  -1.115
+ATOM     25  CA  SER    14      27.615 -27.588   0.272
+ATOM     26  CB  SER    14      27.427 -28.765  -0.269
+ATOM     27  CA  GLY    15      30.990 -25.803   0.598
+ATOM     28  CA  ARG    16      33.226 -28.503   2.118
+ATOM     29  CB  ARG    16      31.258 -30.267  -0.060
+ATOM     30  CA  PRO    17      37.006 -28.439   2.570
+ATOM     31  CB  PRO    17      36.647 -29.128   3.762
+ATOM     32  CA  PRO    18      37.803 -29.734  -0.964
+ATOM     33  CB  PRO    18      37.080 -28.569  -1.350
+ATOM     34  CA  PRO    19      41.472 -30.518  -0.041
+ATOM     35  CB  PRO    19      40.804 -31.161   1.037
+ATOM     36  CA  SER    20      42.993 -31.298  -3.438
+ATOM     37  CB  SER    20      42.128 -30.715  -4.231
+TER
+CONECT    1    3    2
+CONECT    3    5    4
+CONECT    5    7    6
+CONECT    7    9    8
+CONECT    9   11   10
+CONECT   11   13   12
+CONECT   13   15   14
+CONECT   15   17   16
+CONECT   17   19   18
+CONECT   19   20
+CONECT   20   21
+CONECT   21   23   22
+CONECT   23   25   24
+CONECT   25   27   26
+CONECT   27   28
+CONECT   28   30   29
+CONECT   30   32   31
+CONECT   32   34   33
+CONECT   34   36   35
+CONECT   36   37
+ENDMDL
+REMARK Structure   222                                    ENERGY    -2.72223E+01
+ATOM      1  CA  ASN     1       1.902  -0.096   1.799
+ATOM      2  CB  ASN     1       2.937  -0.100   3.520
+ATOM      3  CA  LEU     2       2.387  -3.862   1.700
+ATOM      4  CB  LEU     2       2.171  -5.588   0.557
+ATOM      5  CA  TYR     3       6.088  -4.124   0.901
+ATOM      6  CB  TYR     3       6.748  -1.191   2.387
+ATOM      7  CA  ILE     4       6.224  -7.956   0.885
+ATOM      8  CB  ILE     4       5.434  -9.616   0.377
+ATOM      9  CA  GLN     5       9.923  -8.187  -0.076
+ATOM     10  CB  GLN     5      10.246  -5.959   0.815
+ATOM     11  CA  TRP     6       9.897 -12.022   0.034
+ATOM     12  CB  TRP     6       7.175 -14.485  -0.181
+ATOM     13  CA  LEU     7      13.526 -12.193  -1.104
+ATOM     14  CB  LEU     7      13.798 -10.202  -0.547
+ATOM     15  CA  LYS     8      13.711 -16.024  -0.912
+ATOM     16  CB  LYS     8      11.339 -15.878  -2.203
+ATOM     17  CA  ASP     9      17.273 -16.222  -2.326
+ATOM     18  CB  ASP     9      18.137 -14.676  -1.335
+ATOM     19  CA  GLY    10      17.489 -20.035  -1.950
+ATOM     20  CA  GLY    11      21.018 -20.720  -3.280
+ATOM     21  CA  PRO    12      21.983 -24.404  -2.668
+ATOM     22  CB  PRO    12      21.416 -24.542  -3.964
+ATOM     23  CA  SER    13      25.509 -24.838  -1.309
+ATOM     24  CB  SER    13      25.736 -23.563  -1.114
+ATOM     25  CA  SER    14      27.627 -27.583   0.277
+ATOM     26  CB  SER    14      27.443 -28.762  -0.262
+ATOM     27  CA  GLY    15      30.996 -25.784   0.595
+ATOM     28  CA  ARG    16      33.246 -28.473   2.116
+ATOM     29  CB  ARG    16      31.280 -30.249  -0.054
+ATOM     30  CA  PRO    17      37.026 -28.388   2.562
+ATOM     31  CB  PRO    17      36.672 -29.078   3.755
+ATOM     32  CA  PRO    18      37.825 -29.681  -0.972
+ATOM     33  CB  PRO    18      37.095 -28.520  -1.358
+ATOM     34  CA  PRO    19      41.499 -30.444  -0.055
+ATOM     35  CB  PRO    19      40.837 -31.091   1.025
+ATOM     36  CA  SER    20      43.021 -31.217  -3.453
+ATOM     37  CB  SER    20      42.155 -30.634  -4.246
+TER
+CONECT    1    3    2
+CONECT    3    5    4
+CONECT    5    7    6
+CONECT    7    9    8
+CONECT    9   11   10
+CONECT   11   13   12
+CONECT   13   15   14
+CONECT   15   17   16
+CONECT   17   19   18
+CONECT   19   20
+CONECT   20   21
+CONECT   21   23   22
+CONECT   23   25   24
+CONECT   25   27   26
+CONECT   27   28
+CONECT   28   30   29
+CONECT   30   32   31
+CONECT   32   34   33
+CONECT   34   36   35
+CONECT   36   37
+ENDMDL
+REMARK Structure   254                                    ENERGY    -2.72230E+01
+ATOM      1  CA  ASN     1       1.890  -0.117   1.793
+ATOM      2  CB  ASN     1       2.926  -0.118   3.512
+ATOM      3  CA  LEU     2       2.375  -3.882   1.701
+ATOM      4  CB  LEU     2       2.158  -5.611   0.561
+ATOM      5  CA  TYR     3       6.075  -4.146   0.897
+ATOM      6  CB  TYR     3       6.735  -1.210   2.377
+ATOM      7  CA  ILE     4       6.212  -7.978   0.888
+ATOM      8  CB  ILE     4       5.421  -9.639   0.383
+ATOM      9  CA  GLN     5       9.910  -8.209  -0.078
+ATOM     10  CB  GLN     5      10.233  -5.980   0.809
+ATOM     11  CA  TRP     6       9.885 -12.044   0.039
+ATOM     12  CB  TRP     6       7.163 -14.508  -0.168
+ATOM     13  CA  LEU     7      13.513 -12.215  -1.103
+ATOM     14  CB  LEU     7      13.785 -10.223  -0.550
+ATOM     15  CA  LYS     8      13.700 -16.046  -0.904
+ATOM     16  CB  LYS     8      11.326 -15.904  -2.192
+ATOM     17  CA  ASP     9      17.260 -16.243  -2.324
+ATOM     18  CB  ASP     9      18.124 -14.693  -1.337
+ATOM     19  CA  GLY    10      17.482 -20.055  -1.941
+ATOM     20  CA  GLY    11      21.010 -20.736  -3.276
+ATOM     21  CA  PRO    12      21.983 -24.418  -2.660
+ATOM     22  CB  PRO    12      21.415 -24.559  -3.955
+ATOM     23  CA  SER    13      25.511 -24.840  -1.305
+ATOM     24  CB  SER    13      25.736 -23.564  -1.112
+ATOM     25  CA  SER    14      27.642 -27.576   0.282
+ATOM     26  CB  SER    14      27.460 -28.757  -0.255
+ATOM     27  CA  GLY    15      31.004 -25.764   0.593
+ATOM     28  CA  ARG    16      33.267 -28.442   2.114
+ATOM     29  CB  ARG    16      31.303 -30.230  -0.048
+ATOM     30  CA  PRO    17      37.047 -28.338   2.554
+ATOM     31  CB  PRO    17      36.698 -29.029   3.748
+ATOM     32  CA  PRO    18      37.847 -29.630  -0.981
+ATOM     33  CB  PRO    18      37.111 -28.474  -1.366
+ATOM     34  CA  PRO    19      41.526 -30.376  -0.069
+ATOM     35  CB  PRO    19      40.868 -31.025   1.012
+ATOM     36  CA  SER    20      43.048 -31.144  -3.469
+ATOM     37  CB  SER    20      42.182 -30.560  -4.261
+TER
+CONECT    1    3    2
+CONECT    3    5    4
+CONECT    5    7    6
+CONECT    7    9    8
+CONECT    9   11   10
+CONECT   11   13   12
+CONECT   13   15   14
+CONECT   15   17   16
+CONECT   17   19   18
+CONECT   19   20
+CONECT   20   21
+CONECT   21   23   22
+CONECT   23   25   24
+CONECT   25   27   26
+CONECT   27   28
+CONECT   28   30   29
+CONECT   30   32   31
+CONECT   32   34   33
+CONECT   34   36   35
+CONECT   36   37
+ENDMDL
+REMARK Structure   286                                    ENERGY    -2.72237E+01
+ATOM      1  CA  ASN     1       1.876  -0.138   1.785
+ATOM      2  CB  ASN     1       2.913  -0.136   3.505
+ATOM      3  CA  LEU     2       2.361  -3.904   1.701
+ATOM      4  CB  LEU     2       2.143  -5.635   0.565
+ATOM      5  CA  TYR     3       6.060  -4.168   0.893
+ATOM      6  CB  TYR     3       6.721  -1.229   2.367
+ATOM      7  CA  ILE     4       6.198  -8.000   0.891
+ATOM      8  CB  ILE     4       5.408  -9.662   0.391
+ATOM      9  CA  GLN     5       9.895  -8.232  -0.079
+ATOM     10  CB  GLN     5      10.219  -6.000   0.802
+ATOM     11  CA  TRP     6       9.873 -12.066   0.045
+ATOM     12  CB  TRP     6       7.151 -14.531  -0.154
+ATOM     13  CA  LEU     7      13.499 -12.237  -1.102
+ATOM     14  CB  LEU     7      13.771 -10.243  -0.553
+ATOM     15  CA  LYS     8      13.690 -16.067  -0.896
+ATOM     16  CB  LYS     8      11.314 -15.930  -2.181
+ATOM     17  CA  ASP     9      17.248 -16.262  -2.321
+ATOM     18  CB  ASP     9      18.110 -14.708  -1.339
+ATOM     19  CA  GLY    10      17.476 -20.073  -1.932
+ATOM     20  CA  GLY    11      21.003 -20.751  -3.271
+ATOM     21  CA  PRO    12      21.985 -24.429  -2.651
+ATOM     22  CB  PRO    12      21.414 -24.574  -3.945
+ATOM     23  CA  SER    13      25.516 -24.841  -1.301
+ATOM     24  CB  SER    13      25.737 -23.564  -1.110
+ATOM     25  CA  SER    14      27.657 -27.568   0.287
+ATOM     26  CB  SER    14      27.478 -28.750  -0.247
+ATOM     27  CA  GLY    15      31.013 -25.744   0.591
+ATOM     28  CA  ARG    16      33.289 -28.411   2.111
+ATOM     29  CB  ARG    16      31.327 -30.210  -0.044
+ATOM     30  CA  PRO    17      37.069 -28.291   2.545
+ATOM     31  CB  PRO    17      36.726 -28.982   3.740
+ATOM     32  CA  PRO    18      37.869 -29.582  -0.990
+ATOM     33  CB  PRO    18      37.127 -28.429  -1.375
+ATOM     34  CA  PRO    19      41.553 -30.311  -0.084
+ATOM     35  CB  PRO    19      40.900 -30.962   0.999
+ATOM     36  CA  SER    20      43.074 -31.075  -3.485
+ATOM     37  CB  SER    20      42.208 -30.491  -4.276
+TER
+CONECT    1    3    2
+CONECT    3    5    4
+CONECT    5    7    6
+CONECT    7    9    8
+CONECT    9   11   10
+CONECT   11   13   12
+CONECT   13   15   14
+CONECT   15   17   16
+CONECT   17   19   18
+CONECT   19   20
+CONECT   20   21
+CONECT   21   23   22
+CONECT   23   25   24
+CONECT   25   27   26
+CONECT   27   28
+CONECT   28   30   29
+CONECT   30   32   31
+CONECT   32   34   33
+CONECT   34   36   35
+CONECT   36   37
+ENDMDL
+REMARK Structure   318                                    ENERGY    -2.72244E+01
+ATOM      1  CA  ASN     1       1.861  -0.160   1.778
+ATOM      2  CB  ASN     1       2.898  -0.154   3.496
+ATOM      3  CA  LEU     2       2.346  -3.926   1.700
+ATOM      4  CB  LEU     2       2.128  -5.659   0.568
+ATOM      5  CA  TYR     3       6.045  -4.191   0.888
+ATOM      6  CB  TYR     3       6.705  -1.248   2.356
+ATOM      7  CA  ILE     4       6.184  -8.022   0.894
+ATOM      8  CB  ILE     4       5.394  -9.686   0.398
+ATOM      9  CA  GLN     5       9.880  -8.254  -0.081
+ATOM     10  CB  GLN     5      10.203  -6.020   0.796
+ATOM     11  CA  TRP     6       9.860 -12.088   0.051
+ATOM     12  CB  TRP     6       7.140 -14.555  -0.140
+ATOM     13  CA  LEU     7      13.485 -12.258  -1.100
+ATOM     14  CB  LEU     7      13.756 -10.263  -0.556
+ATOM     15  CA  LYS     8      13.680 -16.087  -0.888
+ATOM     16  CB  LYS     8      11.302 -15.955  -2.168
+ATOM     17  CA  ASP     9      17.237 -16.280  -2.317
+ATOM     18  CB  ASP     9      18.097 -14.723  -1.341
+ATOM     19  CA  GLY    10      17.470 -20.090  -1.922
+ATOM     20  CA  GLY    11      20.997 -20.764  -3.265
+ATOM     21  CA  PRO    12      21.987 -24.439  -2.642
+ATOM     22  CB  PRO    12      21.415 -24.587  -3.935
+ATOM     23  CA  SER    13      25.521 -24.840  -1.296
+ATOM     24  CB  SER    13      25.740 -23.562  -1.108
+ATOM     25  CA  SER    14      27.673 -27.558   0.292
+ATOM     26  CB  SER    14      27.497 -28.742  -0.240
+ATOM     27  CA  GLY    15      31.024 -25.723   0.588
+ATOM     28  CA  ARG    16      33.312 -28.380   2.109
+ATOM     29  CB  ARG    16      31.351 -30.189  -0.039
+ATOM     30  CA  PRO    17      37.092 -28.244   2.536
+ATOM     31  CB  PRO    17      36.753 -28.936   3.732
+ATOM     32  CA  PRO    18      37.891 -29.535  -0.999
+ATOM     33  CB  PRO    18      37.144 -28.386  -1.384
+ATOM     34  CA  PRO    19      41.580 -30.248  -0.099
+ATOM     35  CB  PRO    19      40.931 -30.901   0.985
+ATOM     36  CA  SER    20      43.099 -31.010  -3.501
+ATOM     37  CB  SER    20      42.233 -30.425  -4.292
+TER
+CONECT    1    3    2
+CONECT    3    5    4
+CONECT    5    7    6
+CONECT    7    9    8
+CONECT    9   11   10
+CONECT   11   13   12
+CONECT   13   15   14
+CONECT   15   17   16
+CONECT   17   19   18
+CONECT   19   20
+CONECT   20   21
+CONECT   21   23   22
+CONECT   23   25   24
+CONECT   25   27   26
+CONECT   27   28
+CONECT   28   30   29
+CONECT   30   32   31
+CONECT   32   34   33
+CONECT   34   36   35
+CONECT   36   37
+ENDMDL

diff --git a/examples/unres/MD/ff_1l2y_1le1/MREMD/unres.csh b/examples/unres/MD/ff_1l2y_1le1/MREMD/unres.csh
index 4d31ae5..7176975 100755 (executable)
--- a/examples/unres/MD/ff_1l2y_1le1/MREMD/unres.csh
+++ b/examples/unres/MD/ff_1l2y_1le1/MREMD/unres.csh
@@ -2,7 +2,7 @@
 setenv FGPROCS 1
 setenv POT GB
 setenv PREFIX 1L2Y_MREMD
-setenv OUT1FILE NO
+setenv OUT1FILE YES
 #-----------------------------------------------------------------------------
 setenv UNRES_BIN /users/adam/unres/bin/unres/MD/unres_ifort_MPICH_E0LL2Y.exe
 #-----------------------------------------------------------------------------

diff --git a/source/xdrfpdb/src/geomout.o b/source/xdrfpdb/src/geomout.o
new file mode 100644 (file)
index 0000000..2271cf8
Binary files /dev/null and b/source/xdrfpdb/src/geomout.o differ

diff --git a/source/xdrfpdb/src/xdrf2pdb-m.F b/source/xdrfpdb/src/xdrf2pdb-m.F
index 6a116ee..edbd0d8 100644 (file)
--- a/source/xdrfpdb/src/xdrf2pdb-m.F
+++ b/source/xdrfpdb/src/xdrf2pdb-m.F
@@ -10,17 +10,18 @@
       character*3 sequenc(maxres)
       character*50 tytul
       character*8 onethree,cfreq,cntraj,citraj
+      character*3 licz
       character*8 ucase
       external ucase
-      logical oneletter
+      logical oneletter,iblnk
       integer rescode
       external rescode
       
       ifreq=1
-      if (iargc().lt.3) then
+      if (iargc().lt.5) then
         print '(2a)',
-     &   "Usage: xdrf2pdb-m one/three seqfile cxfile [freq] [pdbfile] ",
-     &    " [ntraj] [itraj]"
+     &   "Usage: xdrf2pdb-m one/three seqfile cxfile ntraj itraj",
+     &   " [pdbfile] [freq]"
         stop
       endif
       call getarg(1,onethree)
@@ -59,7 +60,7 @@
           itype(i)=rescode(i,sequenc(i),0)
         enddo
         print *,nres
-        print '(a3,1x)',(sequenc(i),i=1,nres)
+        print '(20(a3,1x))',(sequenc(i),i=1,nres)
       endif
       call getarg(3,arg)
       iext = index(arg,'.cx') - 1
@@ -67,28 +68,21 @@
         print *,"Error - not a cx file"
         stop
       endif
-      if (iargc().gt.3) then
-        call getarg(4,cfreq)
-        read (cfreq,*) ifreq
-      endif
-      if (iargc().gt.4) then
-        call getarg(5,pdbfile)
-      else
-        pdbfile=arg(:iext)//'.pdb'
-      endif
+      call getarg(4,cntraj)
+      read (cntraj,*) ntraj
+      call getarg(5,citraj)
+      read (citraj,*) itraj
       if (iargc().gt.5) then
-        call getarg(6,cntraj)
-        read (cntraj,*) ntraj
+        call getarg(6,pdbfile)
       else
-        ntraj=1
+        write(licz,'(bz,i3.3)') itraj
+        pdbfile=arg(:iext)//'_'//licz//'.pdb'
       endif
       if (iargc().gt.6) then
-        call getarg(7,citraj)
-        read (citraj,*) itraj
-      else
-        itraj=1
+        call getarg(7,cfreq)
+        read (cfreq,*) ifreq
       endif
-      print *,"ifreq",ifreq," ntraj",ntraj," itraj",itraj
+c      print *,"ifreq",ifreq," ntraj",ntraj," itraj",itraj
       open(9,file=pdbfile)
       nnt = 1
       if (itype(1).eq.21) nnt = 2

diff --git a/source/xdrfpdb/src/xdrf2pdb-m.o b/source/xdrfpdb/src/xdrf2pdb-m.o
new file mode 100644 (file)
index 0000000..4ec1467
Binary files /dev/null and b/source/xdrfpdb/src/xdrf2pdb-m.o differ