Hi Andrew, I guess you want a link between the chains. In that case you'll need to use the option -merge.
Cheers, Tsjerk On Sat, May 16, 2015 at 8:46 PM, Andrew Bostick <andrew.bosti...@gmail.com> wrote: > After using pdb2gmx, my terminal output is as follows: > > Using the Gromos43a1 force field in directory gromos43a1.ff > > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/watermodels.dat > > Select the Water Model: > 1: SPC simple point charge, recommended > 2: SPC/E extended simple point charge > 3: None > 1 > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.r2b > Reading be_near.pdb... > Read 2585 atoms > Analyzing pdb file > Splitting PDB chains based on TER records or changing chain id. > There are 2 chains and 0 blocks of water and 551 residues with 2585 atoms > > chain #res #atoms > 1 'B' 215 1710 > 2 'E' 117 875 > > All occupancies are one > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/atomtypes.atp > Atomtype 1 > Reading residue database... (gromos43a1) > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.rtp > Residue 98 > Sorting it all out... > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.hdb > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.n.tdb > Opening force field file > /usr/local/gromacs/share/gromacs/top/gromos43a1.ff/aminoacids.c.tdb > > Back Off! I just backed up topol.top to ./#topol.top.1# > Processing chain 1 'B' (1710 atoms, 215 residues) > There are 322 donors and 327 acceptors > There are 518 hydrogen bonds > Will use HISE for residue 276 > Will use HISE for residue 301 > Will use HISE for residue 420 > Will use HISE for residue 424 > Will use HISE for residue 426 > Will use HISE for residue 427 > Will use HISE for residue 434 > Identified residue PRO220 as a starting terminus. > Identified residue HIS434 as a ending terminus. > 9 out of 9 lines of specbond.dat converted successfully > Special Atom Distance matrix: > CYS221 CYS223 GLU227 LYS237 LYS239 LYS249 CYS252 > SG13 SG27 CD53 NZ134 NZ150 NZ226 SG248 > CYS223 SG27 0.510 > GLU227 CD53 1.444 1.406 > LYS237 NZ134 3.625 3.530 3.793 > LYS239 NZ150 4.148 4.082 4.362 0.606 > LYS249 NZ226 3.633 3.625 3.499 1.129 1.354 > CYS252 SG248 2.066 2.153 2.028 2.061 2.536 1.649 > LYS259 NZ298 3.093 2.923 1.874 3.475 4.009 2.975 2.346 > GLU263 CD328 3.069 3.158 2.308 2.930 3.325 2.019 1.474 > GLU274 CD425 2.622 2.907 2.615 2.866 3.168 2.174 1.221 > HIS276 NE2444 3.347 3.624 3.268 3.015 3.203 2.171 1.766 > GLU284 CD506 2.957 2.948 2.046 2.858 3.320 2.086 1.525 > GLU285 CD515 3.076 2.982 2.460 2.030 2.510 1.410 1.396 > MET300 SD635 3.692 3.889 3.960 2.150 2.131 1.664 1.995 > HIS301 NE2646 3.819 3.906 4.086 1.358 1.240 1.199 2.064 > LYS308 NZ706 3.118 3.374 3.601 2.409 2.513 2.107 1.798 > GLU309 CD713 2.138 2.447 2.779 2.674 2.972 2.464 1.384 > LYS311 NZ735 1.714 2.056 2.304 2.882 3.256 2.625 1.242 > CYS312 SG743 2.082 2.214 2.050 2.199 2.647 1.726 0.203 > GLU324 CD828 1.606 1.936 1.980 2.934 3.347 2.588 1.074 > LYS325 NZ839 1.399 1.432 1.731 2.303 2.828 2.237 0.780 > LYS329 NZ869 3.010 3.072 3.668 1.475 1.628 1.938 1.912 > LYS331 NZ885 2.095 2.230 3.066 2.322 2.639 2.642 1.806 > LYS333 NZ898 3.201 3.360 4.217 2.653 2.718 3.098 2.748 > LYS346 NZ1001 6.138 5.902 6.647 3.467 3.269 4.536 5.334 > GLU347 CD1008 5.388 5.108 5.909 3.153 3.129 4.262 4.809 > MET349 SD1026 6.176 5.912 6.574 3.426 3.260 4.462 5.315 > LYS351 NZ1041 5.381 5.050 5.656 3.045 3.104 4.056 4.684 > LYS353 NZ1058 5.609 5.319 5.671 2.665 2.624 3.502 4.490 > CYS358 SG1094 4.478 4.345 4.996 1.599 1.405 2.677 3.416 > MET359 SD1099 4.296 4.129 4.999 2.193 2.178 3.298 3.666 > GLU366 CD1159 2.694 2.640 3.428 1.549 1.871 2.269 2.015 > GLU371 CD1198 4.089 3.993 4.364 0.608 0.350 1.598 2.618 > GLU380 CD1269 4.929 4.724 4.913 1.570 1.489 2.243 3.461 > LYS383 NZ1300 4.109 3.853 4.198 1.347 1.602 2.244 2.969 > MET389 SD1346 2.803 2.714 3.788 2.344 2.614 3.148 2.730 > LYS400 NZ1437 4.512 4.242 4.802 1.907 2.005 2.956 3.609 > LYS405 NZ1478 6.045 5.762 6.299 3.180 3.053 4.149 5.075 > GLU409 CD1513 6.268 6.022 6.532 3.171 2.938 4.100 5.161 > CYS416 SG1565 4.478 4.352 4.951 1.453 1.218 2.512 3.327 > HIS420 NE21594 3.511 3.512 4.225 1.534 1.535 2.311 2.546 > GLU421 CD1601 3.375 3.423 4.043 1.485 1.504 2.067 2.269 > HIS424 NE21625 4.712 4.746 5.439 2.326 1.981 3.030 3.638 > HIS426 NE21643 3.940 4.027 4.508 1.663 1.449 2.036 2.585 > HIS427 NE21653 4.616 4.578 5.023 1.368 0.849 2.110 3.164 > GLU429 CD1667 4.903 4.846 5.320 1.621 1.099 2.406 3.492 > LYS430 NZ1678 4.918 4.813 5.540 2.168 1.875 3.185 3.923 > HIS434 NE21708 6.201 5.991 6.588 3.125 2.832 4.102 5.125 > LYS259 GLU263 GLU274 HIS276 GLU284 GLU285 MET300 > NZ298 CD328 CD425 NE2444 CD506 CD515 SD635 > GLU263 CD328 1.809 > GLU274 CD425 3.077 1.556 > HIS276 NE2444 3.462 1.729 0.726 > GLU284 CD506 1.216 0.623 2.004 2.284 > GLU285 CD515 1.567 1.273 2.237 2.490 0.927 > MET300 SD635 4.078 2.600 1.658 1.426 2.974 2.701 > HIS301 NE2646 4.001 2.813 2.234 2.142 3.030 2.490 0.899 > LYS308 NZ706 4.084 2.694 1.401 1.456 3.049 2.872 0.797 > GLU309 CD713 3.650 2.528 1.205 1.714 2.786 2.745 1.717 > LYS311 NZ735 3.330 2.338 1.160 1.814 2.552 2.629 2.116 > CYS312 SG743 2.427 1.421 1.023 1.594 1.548 1.514 1.925 > GLU324 CD828 2.999 2.045 1.048 1.762 2.242 2.411 2.262 > LYS325 NZ839 2.514 2.115 1.765 2.412 2.029 1.880 2.529 > LYS329 NZ869 4.051 3.203 2.396 2.655 3.296 2.760 1.668 > LYS331 NZ885 3.945 3.254 2.281 2.774 3.320 2.998 2.270 > LYS333 NZ898 4.995 4.098 2.944 3.225 4.251 3.851 2.308 > LYS346 NZ1001 6.400 6.347 6.200 6.373 6.158 5.261 5.202 > GLU347 CD1008 5.766 5.890 5.783 6.057 5.643 4.774 5.018 > MET349 SD1026 6.193 6.244 6.231 6.404 6.017 5.105 5.293 > LYS351 NZ1041 5.240 5.580 5.746 6.019 5.256 4.369 5.121 > LYS353 NZ1058 4.931 5.138 5.471 5.625 4.845 3.924 4.738 > CYS358 SG1094 4.899 4.495 4.174 4.335 4.411 3.577 3.168 > MET359 SD1099 5.149 4.909 4.494 4.771 4.782 3.993 3.681 > GLU366 CD1159 3.881 3.411 2.813 3.212 3.360 2.769 2.425 > GLU371 CD1198 4.066 3.505 3.339 3.434 3.456 2.623 2.371 > GLU380 CD1269 4.133 4.003 4.321 4.393 3.801 2.880 3.534 > LYS383 NZ1300 3.671 3.761 4.007 4.247 3.482 2.574 3.495 > MET389 SD1346 4.476 4.177 3.503 3.958 4.091 3.539 3.191 > LYS400 NZ1437 4.453 4.550 4.625 4.881 4.289 3.398 3.977 > LYS405 NZ1478 5.753 5.886 6.027 6.189 5.627 4.705 5.160 > GLU409 CD1513 5.962 5.940 6.031 6.131 5.731 4.806 5.030 > CYS416 SG1565 4.805 4.365 4.068 4.206 4.291 3.452 3.034 > HIS420 NE21594 4.531 3.818 3.101 3.320 3.860 3.218 2.189 > GLU421 CD1601 4.359 3.508 2.719 2.912 3.603 3.017 1.778 > HIS424 NE21625 5.639 4.755 3.960 3.993 4.872 4.207 2.623 > HIS426 NE21643 4.679 3.621 2.804 2.814 3.800 3.227 1.465 > HIS427 NE21653 4.828 4.061 3.665 3.658 4.108 3.333 2.370 > GLU429 CD1667 5.089 4.379 4.014 4.003 4.406 3.606 2.706 > LYS430 NZ1678 5.524 5.033 4.580 4.705 4.991 4.178 3.438 > HIS434 NE21708 6.168 6.003 5.930 6.020 5.845 4.932 4.831 > HIS301 LYS308 GLU309 LYS311 CYS312 GLU324 LYS325 > NE2646 NZ706 CD713 NZ735 SG743 CD828 NZ839 > LYS308 NZ706 1.405 > GLU309 CD713 2.128 1.018 > LYS311 NZ735 2.500 1.486 0.516 > CYS312 SG743 2.082 1.700 1.274 1.122 > GLU324 CD828 2.633 1.722 0.850 0.381 0.940 > LYS325 NZ839 2.523 2.149 1.441 1.188 0.879 1.072 > LYS329 NZ869 1.295 1.463 1.656 2.013 1.969 2.242 1.938 > LYS331 NZ885 2.234 1.693 1.201 1.399 1.836 1.677 1.465 > LYS333 NZ898 2.250 1.810 1.864 2.266 2.754 2.611 2.587 > LYS346 NZ1001 4.349 5.365 5.612 5.868 5.490 6.016 5.229 > GLU347 CD1008 4.197 5.078 5.154 5.342 4.979 5.467 4.597 > MET349 SD1026 4.417 5.495 5.726 5.952 5.481 6.068 5.233 > LYS351 NZ1041 4.276 5.254 5.296 5.422 4.871 5.478 4.525 > LYS353 NZ1058 3.860 5.041 5.242 5.392 4.668 5.416 4.530 > CYS358 SG1094 2.341 3.313 3.611 3.903 3.550 4.064 3.407 > MET359 SD1099 2.954 3.642 3.741 3.992 3.806 4.176 3.461 > GLU366 CD1159 1.980 2.163 2.012 2.214 2.130 2.394 1.764 > GLU371 CD1198 1.492 2.668 3.044 3.315 2.745 3.415 2.816 > GLU380 CD1269 2.675 3.931 4.240 4.418 3.618 4.431 3.674 > LYS383 NZ1300 2.693 3.690 3.764 3.874 3.153 3.883 2.987 > MET389 SD1346 2.796 2.815 2.526 2.687 2.839 2.900 2.285 > LYS400 NZ1437 3.143 4.116 4.199 4.350 3.789 4.414 3.516 > LYS405 NZ1478 4.270 5.414 5.637 5.833 5.248 5.910 5.042 > GLU409 CD1513 4.133 5.341 5.665 5.902 5.322 5.995 5.194 > CYS416 SG1565 2.190 3.220 3.553 3.849 3.458 4.003 3.361 > HIS420 NE21594 1.627 2.090 2.338 2.691 2.629 2.925 2.506 > GLU421 CD1601 1.293 1.674 1.999 2.383 2.329 2.621 2.313 > HIS424 NE21625 2.070 2.709 3.266 3.706 3.693 3.975 3.711 > HIS426 NE21643 0.958 1.611 2.271 2.717 2.614 2.953 2.807 > HIS427 NE21653 1.524 2.714 3.286 3.652 3.255 3.818 3.385 > GLU429 CD1667 1.866 3.054 3.621 3.986 3.588 4.154 3.689 > LYS430 NZ1678 2.657 3.571 3.939 4.278 4.040 4.481 3.904 > HIS434 NE21708 3.951 5.112 5.476 5.753 5.274 5.885 5.144 > LYS329 LYS331 LYS333 LYS346 GLU347 MET349 LYS351 > NZ869 NZ885 NZ898 NZ1001 CD1008 SD1026 NZ1041 > LYS331 NZ885 1.101 > LYS333 NZ898 1.207 1.167 > LYS346 NZ1001 3.996 4.683 4.452 > GLU347 CD1008 3.640 4.154 4.117 0.988 > MET349 SD1026 4.140 4.838 4.717 0.545 1.030 > LYS351 NZ1041 3.884 4.412 4.594 1.612 1.026 1.259 > LYS353 NZ1058 3.843 4.571 4.759 2.042 1.924 1.601 1.192 > CYS358 SG1094 1.978 2.819 2.649 2.059 1.911 2.197 2.256 > MET359 SD1099 2.194 2.728 2.566 1.985 1.555 2.220 2.164 > GLU366 CD1159 0.825 1.054 1.516 3.686 3.155 3.806 3.379 > GLU371 CD1198 1.601 2.573 2.657 2.983 2.796 2.982 2.799 > GLU380 CD1269 2.945 3.793 4.017 2.762 2.645 2.512 2.198 > LYS383 NZ1300 2.528 3.153 3.556 2.750 2.275 2.550 1.848 > MET389 SD1346 1.547 1.340 1.592 3.623 3.002 3.814 3.403 > LYS400 NZ1437 2.781 3.390 3.607 1.951 1.414 1.786 1.150 > LYS405 NZ1478 4.107 4.829 4.837 1.184 1.338 0.674 1.000 > GLU409 CD1513 4.093 4.909 4.815 1.177 1.661 0.802 1.534 > CYS416 SG1565 1.927 2.819 2.667 2.177 2.060 2.286 2.335 > HIS420 NE21594 0.711 1.566 1.312 3.360 3.064 3.553 3.432 > GLU421 CD1601 0.388 1.411 1.214 3.733 3.450 3.904 3.757 > HIS424 NE21625 1.786 2.662 1.894 3.184 3.253 3.488 3.804 > HIS426 NE21643 0.973 1.994 1.577 3.901 3.789 4.079 4.092 > HIS427 NE21653 1.753 2.827 2.550 2.915 2.959 3.027 3.178 > GLU429 CD1667 2.057 3.110 2.783 2.644 2.780 2.768 3.034 > LYS430 NZ1678 2.286 3.119 2.708 1.897 1.974 2.177 2.546 > HIS434 NE21708 3.851 4.685 4.456 0.845 1.560 0.810 1.813 > LYS353 CYS358 MET359 GLU366 GLU371 GLU380 LYS383 > NZ1058 SG1094 SD1099 CD1159 CD1198 CD1269 NZ1300 > CYS358 SG1094 2.244 > MET359 SD1099 2.604 0.905 > GLU366 CD1159 3.535 1.841 1.785 > GLU371 CD1198 2.413 1.100 1.851 1.705 > GLU380 CD1269 1.322 1.830 2.515 2.850 1.397 > LYS383 NZ1300 1.544 1.639 2.011 2.176 1.369 1.032 > MET389 SD1346 3.838 2.124 1.663 0.884 2.385 3.420 2.646 > LYS400 NZ1437 1.284 1.335 1.480 2.343 1.688 1.432 0.862 > LYS405 NZ1478 0.964 2.237 2.415 3.777 2.797 2.047 2.173 > GLU409 CD1513 1.195 2.173 2.501 3.871 2.718 2.010 2.354 > CYS416 SG1565 2.221 0.203 1.099 1.851 0.923 1.697 1.579 > HIS420 NE21594 3.473 1.394 1.570 0.912 1.399 2.731 2.344 > GLU421 CD1601 3.709 1.716 1.982 0.984 1.460 2.842 2.503 > HIS424 NE21625 3.755 1.589 1.926 2.161 1.912 3.100 3.059 > HIS426 NE21643 3.879 1.913 2.390 1.688 1.533 2.902 2.815 > HIS427 NE21653 2.809 1.097 1.918 2.071 0.840 1.918 2.104 > GLU429 CD1667 2.661 1.018 1.865 2.308 1.039 1.889 2.152 > LYS430 NZ1678 2.612 0.647 1.011 2.234 1.628 2.338 2.262 > HIS434 NE21708 1.689 1.882 2.182 3.675 2.603 2.229 2.513 > MET389 LYS400 LYS405 GLU409 CYS416 HIS420 GLU421 > SD1346 NZ1437 NZ1478 CD1513 SG1565 NE21594 CD1601 > LYS400 NZ1437 2.562 > LYS405 NZ1478 3.905 1.538 > GLU409 CD1513 4.057 1.793 0.570 > CYS416 SG1565 2.214 1.372 2.280 2.191 > HIS420 NE21594 1.384 2.388 3.598 3.564 1.384 > GLU421 CD1601 1.606 2.671 3.908 3.857 1.668 0.423 > HIS424 NE21625 2.412 2.916 3.666 3.460 1.579 1.256 1.402 > HIS426 NE21643 2.303 3.009 4.078 3.928 1.817 0.979 0.717 > HIS427 NE21653 2.637 2.181 2.979 2.764 0.929 1.383 1.457 > GLU429 CD1667 2.800 2.118 2.750 2.495 0.864 1.609 1.743 > LYS430 NZ1678 2.370 1.834 2.385 2.233 0.757 1.613 1.958 > HIS434 NE21708 3.809 1.886 1.025 0.634 1.926 3.259 3.574 > HIS424 HIS426 HIS427 GLU429 LYS430 > NE21625 NE21643 NE21653 CD1667 NZ1678 > HIS426 NE21643 1.188 > HIS427 NE21653 1.268 1.228 > GLU429 CD1667 1.310 1.529 0.350 > LYS430 NZ1678 1.322 2.047 1.283 1.096 > HIS434 NE21708 2.998 3.617 2.487 2.184 1.778 > Linking CYS-252 SG-248 and CYS-312 SG-743... > Linking CYS-358 SG-1094 and CYS-416 SG-1565... > Start terminus PRO-220: PRO-NH2+ > End terminus HIS-434: COO- > Checking for duplicate atoms.... > Now there are 215 residues with 2170 atoms > Chain time... > Making bonds... > Number of bonds was 2225, now 2221 > Generating angles, dihedrals and pairs... > Before cleaning: 3579 pairs > Before cleaning: 4281 dihedrals > Making cmap torsions...There are 1188 dihedrals, 1103 impropers, 3254 > angles > 3579 pairs, 2221 bonds and 0 virtual sites > Total mass 24305.633 a.m.u. > Total charge -5.000 e > Writing topology > Processing chain 2 'E' (875 atoms, 117 residues) > There are 186 donors and 177 acceptors > There are 298 hydrogen bonds > Will use HISE for residue 506 > Will use HISE for residue 546 > Identified residue GLY435 as a starting terminus. > Identified residue LYS551 as a ending terminus. > 9 out of 9 lines of specbond.dat converted successfully > Special Atom Distance matrix: > GLU463 GLU470 LYS499 HIS506 GLU520 GLU535 LYS540 > CD205 CD249 NZ469 NE2531 CD628 CD746 NZ789 > GLU470 CD249 1.118 > LYS499 NZ469 1.596 1.306 > HIS506 NE2531 2.138 1.493 1.065 > GLU520 CD628 2.260 3.211 3.593 3.893 > GLU535 CD746 3.466 3.161 2.570 1.821 4.426 > LYS540 NZ789 2.821 2.362 2.493 1.589 3.763 1.550 > HIS546 NE2831 2.133 2.600 2.943 2.795 1.663 3.007 2.204 > LYS551 NZ873 1.393 2.494 2.682 3.242 1.189 4.082 3.598 > HIS546 > NE2831 > LYS551 NZ873 1.997 > Start terminus GLY-435: GLY-NH3+ > End terminus LYS-551: COO- > Checking for duplicate atoms.... > Now there are 117 residues with 1149 atoms > Chain time... > Making bonds... > Number of bonds was 1176, now 1171 > Generating angles, dihedrals and pairs... > Before cleaning: 1840 pairs > Before cleaning: 2295 dihedrals > Making cmap torsions...There are 570 dihedrals, 643 impropers, 1724 > angles > 1840 pairs, 1171 bonds and 0 virtual sites > Total mass 12358.454 a.m.u. > Total charge -1.000 e > Writing topology > Including chain 1 in system: 2170 atoms 215 residues > Including chain 2 in system: 1149 atoms 117 residues > Now there are 3319 atoms and 332 residues > Total mass in system 36664.087 a.m.u. > Total charge in system -6.000 e > > Writing coordinate file... > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Tsjerk A. Wassenaar, Ph.D. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
