[gmx-users] question
Andrew Bostick
andrew.bostick1 at gmail.com
Sat May 16 20:46:03 CEST 2015
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...
More information about the gromacs.org_gmx-users
mailing list