From: Adam Liwo Date: Mon, 11 Jun 2012 14:43:15 +0000 (-0400) Subject: 6/11/2012 by Adam X-Git-Tag: v.3.2~80^2~11^2~4 X-Git-Url: http://mmka.chem.univ.gda.pl/gitweb/?p=unres.git;a=commitdiff_plain;h=f0ab76db798e4461535a3ce519bf1188744a7d9b 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 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 --- 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 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 --- 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 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 --- 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 index 0000000..4ec1467 Binary files /dev/null and b/source/xdrfpdb/src/xdrf2pdb-m.o differ