I ve used this ：gmx pdb2gmx -f 1tub.pdb -o 1tub.gro -water spc -ignh -ter，but I don‘t know what to choose.
PS C:\Users\Administrator\Desktop\weiguandanbai> gmx pdb2gmx -f 1tub.pdb -o 1tub.gro -water spc -ignh -ter
:-) GROMACS - gmx pdb2gmx, 2020.6-MODIFIED (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
Alfons Sijbers Peter Tieleman Jon Vincent Teemu Virolainen
Christian Wennberg Maarten Wolf Artem Zhmurov
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2019, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
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of the License, or (at your option) any later version.
GROMACS: gmx pdb2gmx, version 2020.6-MODIFIED
Executable: D:\gmx2020.6_GPU\bin\gmx.exe
Data prefix: D:\gmx2020.6_GPU
Working dir: C:\Users\Administrator\Desktop\weiguandanbai
Command line:
gmx pdb2gmx -f 1tub.pdb -o 1tub.gro -water spc -ignh -ter
Select the Force Field:
From ‘D:/gmx2020.6_GPU/share/gromacs/top’:
1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
8: CHARMM all-atom force field
9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
10: CHARMM36 all-atom force field
11: GROMOS96 43a1 force field
12: GROMOS96 43a2 force field (improved alkane dihedrals)
13: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
14: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
16: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9)
17: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
8
Using the Charmm36 force field in directory charmm36.ff
going to rename charmm36.ff/aminoacids.r2b
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/aminoacids.r2b
going to rename charmm36.ff/carb.r2b
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/carb.r2b
going to rename charmm36.ff/cgenff.r2b
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/cgenff.r2b
going to rename charmm36.ff/ethers.r2b
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/ethers.r2b
going to rename charmm36.ff/lipid.r2b
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/lipid.r2b
going to rename charmm36.ff/metals.r2b
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/metals.r2b
going to rename charmm36.ff/na.r2b
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/na.r2b
going to rename charmm36.ff/silicates.r2b
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/silicates.r2b
going to rename charmm36.ff/solvent.r2b
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/solvent.r2b
Reading 1tub.pdb…
WARNING: all CONECT records are ignored
Read ‘TUBULIN; TUBULIN’, 6907 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
WARNING: Chain identifier ‘A’ is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
WARNING: Chain identifier ‘B’ is used in two non-sequential blocks.
They will be treated as separate chains unless you reorder your file.
There are 4 chains and 0 blocks of water and 870 residues with 6907 atoms
chain #res #atoms
1 ‘A’ 440 3430
2 ‘B’ 427 3359
3 ‘A’ 1 32
4 ‘B’ 2 86
All occupancies are one
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/atomtypes.atp
Reading residue database… (Charmm36)
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/aminoacids.rtp
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/carb.rtp
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/cgenff.rtp
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/ethers.rtp
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/lipid.rtp
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/metals.rtp
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/na.rtp
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/silicates.rtp
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/solvent.rtp
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/aminoacids.hdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/carb.hdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/cgenff.hdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/ethers.hdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/lipid.hdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/metals.hdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/na.hdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/silicates.hdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/solvent.hdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/aminoacids.n.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/carb.n.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/cgenff.n.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/ethers.n.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/lipid.n.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/metals.n.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/na.n.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/silicates.n.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/solvent.n.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/aminoacids.c.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/carb.c.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/cgenff.c.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/ethers.c.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/lipid.c.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/metals.c.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/na.c.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/silicates.c.tdb
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/solvent.c.tdb
Processing chain 1 ‘A’ (3430 atoms, 440 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 653 donors and 657 acceptors were found.
There are 1004 hydrogen bonds
Will use HISE for residue 8
Will use HISE for residue 28
Will use HISE for residue 61
Will use HISE for residue 88
Will use HISE for residue 107
Will use HISE for residue 139
Will use HISE for residue 192
Will use HISE for residue 197
Will use HISE for residue 266
Will use HISE for residue 283
Will use HISE for residue 309
Will use HISE for residue 393
Will use HISE for residue 406
Identified residue MET1 as a starting terminus.
Identified residue VAL440 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET1 CYS4 HIS8 CYS20 CYS25 HIS28 MET36
SD7 SG34 NE266 SG142 SG191 NE2218 SD274
CYS4 SG34 1.225
HIS8 NE266 2.305 1.259
CYS20 SG142 2.175 1.097 0.678
CYS25 SG191 2.315 1.865 1.536 1.328
HIS28 NE2218 1.056 0.794 1.506 1.243 1.332
MET36 SD274 1.535 1.573 1.689 1.752 1.199 1.027
HIS61 NE2456 1.947 2.003 1.900 2.172 1.666 1.633 0.677
HIS88 NE2679 2.408 1.972 1.382 1.923 1.901 1.952 1.360
HIS107 NE2825 3.508 2.426 2.060 2.335 3.566 3.136 3.555
CYS129 SG1004 1.218 1.194 1.643 1.892 2.130 1.287 1.185
HIS139 NE21081 2.942 1.751 1.526 1.508 2.830 2.405 3.019
MET154 SD1178 2.439 1.309 1.290 1.410 2.658 2.038 2.598
HIS192 NE21480 2.948 1.853 1.722 1.882 3.156 2.591 3.126
HIS197 NE21521 2.622 1.615 1.726 1.883 3.109 2.388 2.941
CYS200 SG1541 2.162 1.309 2.060 1.725 2.846 1.927 2.855
MET203 SD1564 2.866 1.690 1.573 1.254 2.534 2.198 2.929
CYS213 SG1644 3.498 2.542 2.144 1.621 2.096 2.530 3.078
HIS266 NE22071 3.122 2.215 2.656 2.357 3.593 2.849 3.746
HIS283 NE22204 4.051 3.613 3.785 3.131 3.067 3.319 3.967
CYS295 SG2291 2.719 2.112 2.595 1.932 2.485 2.112 3.035
MET302 SD2347 2.918 1.939 1.884 1.272 2.106 2.071 2.827
CYS305 SG2370 3.424 2.382 2.427 1.967 3.070 2.781 3.620
HIS309 NE22406 4.362 3.410 3.525 3.071 4.116 3.812 4.697
MET313 SD2438 3.267 2.530 3.122 2.683 3.771 3.020 4.003
CYS315 SG2450 2.842 2.206 2.862 2.294 3.159 2.484 3.490
CYS316 SG2456 1.957 1.408 2.298 1.767 2.551 1.655 2.678
CYS347 SG2704 3.160 2.613 3.367 2.875 3.826 3.004 4.022
CYS376 SG2915 2.138 1.478 1.977 1.322 1.860 1.415 2.329
MET377 SD2922 2.897 2.160 2.625 2.009 2.815 2.351 3.307
HIS393 NE23047 4.686 3.591 3.460 3.192 4.385 4.126 4.903
MET398 SD3090 4.589 3.375 2.800 2.760 3.921 3.904 4.444
HIS406 NE23161 5.427 4.247 3.594 3.774 4.933 4.865 5.269
MET413 SD3218 4.438 3.405 3.011 3.314 4.528 4.127 4.507
MET425 SD3316 3.596 2.479 2.421 2.297 3.615 3.144 3.868
HIS61 HIS88 HIS107 CYS129 HIS139 MET154 HIS192
NE2456 NE2679 NE2825 SG1004 NE21081 SD1178 NE21480
HIS88 NE2679 1.002
HIS107 NE2825 3.652 2.896
CYS129 SG1004 1.221 1.317 2.876
HIS139 NE21081 3.296 2.737 1.061 2.577
MET154 SD1178 2.828 2.300 1.130 1.987 0.653
HIS192 NE21480 3.311 2.687 0.637 2.460 0.623 0.553
HIS197 NE21521 3.125 2.575 0.955 2.171 0.892 0.479 0.420
CYS200 SG1541 3.306 3.133 2.188 2.401 1.374 1.282 1.565
MET203 SD1564 3.327 2.923 1.757 2.722 0.705 1.127 1.302
CYS213 SG1644 3.566 3.374 3.218 3.486 2.264 2.596 2.865
HIS266 NE22071 4.166 3.848 2.087 3.264 1.408 1.654 1.619
HIS283 NE22204 4.602 4.815 4.991 4.583 3.938 4.158 4.504
CYS295 SG2291 3.664 3.746 3.500 3.245 2.450 2.589 2.940
MET302 SD2347 3.356 3.191 2.792 3.024 1.748 2.028 2.331
CYS305 SG2370 4.100 3.793 2.467 3.520 1.508 1.988 2.066
HIS309 NE22406 5.196 4.891 3.198 4.566 2.424 2.945 2.894
MET313 SD2438 4.509 4.334 2.860 3.660 2.076 2.308 2.368
CYS315 SG2450 4.070 4.049 3.208 3.383 2.244 2.404 2.643
CYS316 SG2456 3.256 3.324 2.995 2.545 2.059 1.985 2.370
CYS347 SG2704 4.570 4.517 3.329 3.735 2.508 2.653 2.791
CYS376 SG2915 2.951 3.049 3.168 2.565 2.150 2.155 2.593
MET377 SD2922 3.898 3.863 3.186 3.346 2.156 2.374 2.644
HIS393 NE23047 5.292 4.789 2.594 4.625 2.130 2.739 2.499
MET398 SD3090 4.697 4.012 1.883 4.188 1.699 2.320 2.027
HIS406 NE23161 5.372 4.522 2.044 4.813 2.538 2.992 2.530
MET413 SD3218 4.540 3.712 0.998 3.765 1.976 2.114 1.587
MET425 SD3316 4.184 3.644 1.370 3.393 0.911 1.439 1.154
HIS197 CYS200 MET203 CYS213 HIS266 HIS283 CYS295
NE21521 SG1541 SD1564 SG1644 NE22071 NE22204 SG2291
CYS200 SG1541 1.408
MET203 SD1564 1.466 1.210
CYS213 SG1644 3.029 2.503 1.653
HIS266 NE22071 1.638 0.967 1.309 2.708
HIS283 NE22204 4.548 3.470 3.242 2.062 3.746
CYS295 SG2291 2.919 1.719 1.802 1.644 2.105 1.763
MET302 SD2347 2.431 1.705 1.065 0.817 1.979 2.202 1.063
CYS305 SG2370 2.235 1.545 0.926 1.592 1.256 2.809 1.520
HIS309 NE22406 3.082 2.354 1.983 2.388 1.701 3.115 2.167
MET313 SD2438 2.355 1.265 1.751 2.747 0.787 3.335 1.779
CYS315 SG2450 2.599 1.267 1.718 2.253 1.399 2.545 0.932
CYS316 SG2456 2.222 0.897 1.634 2.294 1.622 2.769 1.045
CYS347 SG2704 2.720 1.449 2.132 2.936 1.284 3.179 1.667
CYS376 SG2915 2.530 1.501 1.583 1.590 2.151 2.162 0.716
MET377 SD2922 2.651 1.439 1.524 1.741 1.620 2.149 0.550
HIS393 NE23047 2.792 2.596 1.976 2.738 1.794 3.991 2.932
MET398 SD3090 2.430 2.811 1.798 2.553 2.315 4.354 3.319
HIS406 NE23161 2.925 3.768 2.936 3.882 3.242 5.754 4.627
MET413 SD3218 1.849 3.048 2.631 4.040 2.728 5.848 4.385
MET425 SD3316 1.429 1.610 1.118 2.597 1.023 4.109 2.639
MET302 CYS305 HIS309 MET313 CYS315 CYS316 CYS347
SD2347 SG2370 NE22406 SD2438 SG2450 SG2456 SG2704
CYS305 SG2370 1.042
HIS309 NE22406 2.018 1.106
MET313 SD2438 2.013 1.325 1.461
CYS315 SG2450 1.516 1.314 1.743 0.893
CYS316 SG2456 1.516 1.719 2.487 1.476 0.889
CYS347 SG2704 2.193 1.708 1.812 0.565 0.746 1.361
CYS376 SG2915 0.972 1.699 2.600 2.058 1.322 0.885 2.019
MET377 SD2922 1.051 1.086 1.683 1.268 0.530 1.006 1.253
HIS393 NE23047 2.440 1.468 1.096 2.002 2.501 3.040 2.515
MET398 SD3090 2.451 1.879 2.208 2.822 3.140 3.360 3.353
HIS406 NE23161 3.764 3.191 3.434 3.879 4.349 4.482 4.438
MET413 SD3218 3.669 3.181 3.686 3.500 4.002 3.897 4.010
MET425 SD3316 2.070 1.329 1.853 1.705 2.186 2.332 2.246
CYS376 MET377 HIS393 MET398 HIS406 MET413
SG2915 SD2922 NE23047 SD3090 NE23161 SD3218
MET377 SD2922 1.023
HIS393 NE23047 3.162 2.442
MET398 SD3090 3.282 2.950 1.362
HIS406 NE23161 4.508 4.239 2.399 1.409
MET413 SD3218 4.119 4.015 2.852 2.107 1.574
MET425 SD3316 2.577 2.193 1.367 1.379 2.239 1.919
Select start terminus type for MET-1
0: MET1
1: NH3+
2: NH2
3: HYD1
4: 5TER
5: 5MET
6: 5PHO
7: 5POM
8: None
1
Start terminus MET-1: NH3+
Select end terminus type for VAL-440
0: COO-
1: COOH
2: CT2
3: CT1
4: HYD2
5: MET2
6: 3TER
7: None
0
End terminus VAL-440: COO-
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/aminoacids.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Now there are 440 residues with 6764 atoms
Chain time…
Making bonds…
Number of bonds was 6842, now 6842
Generating angles, dihedrals and pairs…
Before cleaning: 17900 pairs
Before cleaning: 18085 dihedrals
Keeping all generated dihedrals
Making cmap torsions…
There are 438 cmap torsion pairs
There are 18085 dihedrals, 1202 impropers, 12336 angles
17774 pairs, 6842 bonds and 0 virtual sites
Total mass 48798.518 a.m.u.
Total charge -18.000 e
Writing topology
Processing chain 2 ‘B’ (3359 atoms, 427 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 648 donors and 647 acceptors were found.
There are 962 hydrogen bonds
Will use HISE for residue 6
Will use HISE for residue 28
Will use HISE for residue 37
Will use HISE for residue 107
Will use HISE for residue 139
Will use HISE for residue 192
Will use HISE for residue 229
Will use HISE for residue 266
Will use HISE for residue 309
Will use HISE for residue 406
Identified residue MET1 as a starting terminus.
Identified residue ASP437 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET1 HIS6 CYS12 HIS28 HIS37 MET75 HIS107
SD7 NE253 SG94 NE2223 NE2289 SD570 NE2816
HIS6 NE253 1.627
CYS12 SG94 3.379 1.905
HIS28 NE2223 1.721 0.823 2.104
HIS37 NE2289 1.526 1.687 3.319 1.236
MET75 SD570 3.317 1.834 1.840 2.417 3.221
HIS107 NE2816 3.244 2.299 1.746 2.860 3.920 2.366
CYS129 SG984 1.180 1.546 3.330 2.062 1.990 2.656 3.063
CYS131 SG998 0.483 1.560 3.235 1.859 1.906 3.132 2.888
HIS139 NE21064 3.007 1.840 0.922 2.162 3.350 2.218 1.025
MET149 SD1118 3.076 1.780 1.319 2.419 3.466 1.404 0.964
MET166 SD1259 1.881 1.282 1.931 1.765 2.666 2.418 1.399
HIS192 NE21456 2.846 1.897 1.459 2.360 3.452 2.340 0.588
CYS203 SG1546 3.072 2.129 1.327 2.075 3.244 2.949 1.907
CYS213 SG1626 3.622 2.340 1.419 1.993 3.060 2.774 3.032
HIS229 NE21758 3.258 1.982 1.855 1.540 2.372 2.477 3.391
MET235 SD1798 2.299 0.976 1.225 0.912 2.147 2.074 2.162
CYS241 SG1836 1.973 1.461 2.306 0.721 1.481 3.031 3.122
MET259 SD1978 2.479 2.169 2.300 1.887 2.761 3.582 2.594
HIS266 NE22040 2.958 2.660 2.456 2.635 3.567 3.820 2.197
MET269 SD2069 3.236 2.349 1.556 2.161 3.292 3.226 2.296
MET295 SD2270 2.910 2.441 2.543 1.793 2.504 3.790 3.481
MET301 SD2319 3.282 2.533 2.039 2.093 3.077 3.594 2.998
MET302 SD2327 2.911 1.847 1.394 1.485 2.620 2.792 2.583
CYS305 SG2344 3.619 2.737 1.716 2.593 3.728 3.475 2.346
HIS309 NE22380 4.436 3.759 2.734 3.547 4.591 4.529 3.160
MET323 SD2490 3.049 2.929 3.430 2.145 2.330 4.405 4.382
MET325 SD2504 2.283 2.559 3.476 1.855 1.838 4.256 4.115
MET332 SD2563 2.957 2.757 2.977 2.120 2.675 4.223 3.737
CYS356 SG2758 1.687 1.659 2.748 0.988 1.322 3.380 3.356
MET373 SD2827 2.970 2.674 3.168 1.868 2.107 4.067 4.231
MET398 SD3022 4.571 3.367 1.698 3.610 4.838 3.162 1.816
HIS406 NE23099 5.202 4.057 2.625 4.505 5.683 3.473 1.989
MET413 SD3156 3.961 2.940 1.928 3.445 4.568 2.728 0.732
MET416 SD3181 4.496 3.729 2.799 4.190 5.280 3.703 1.479
MET425 SD3253 3.682 2.794 1.720 3.008 4.170 3.205 1.352
CYS129 CYS131 HIS139 MET149 MET166 HIS192 CYS203
SG984 SG998 NE21064 SD1118 SD1259 NE21456 SG1546
CYS131 SG998 1.000
HIS139 NE21064 3.050 2.781
MET149 SD1118 2.687 2.774 1.105
MET166 SD1259 1.997 1.578 1.260 1.489
HIS192 NE21456 2.831 2.542 0.593 1.033 0.971
CYS203 SG1546 3.452 2.968 0.986 2.060 1.672 1.392
CYS213 SG1626 3.880 3.665 2.030 2.658 2.735 2.591 1.620
HIS229 NE21758 3.415 3.375 2.481 2.800 2.831 2.951 2.278
MET235 SD1798 2.495 2.269 1.322 1.765 1.421 1.656 1.311
CYS241 SG1836 2.615 2.172 2.312 2.848 2.019 2.561 1.902
MET259 SD1978 3.221 2.484 1.868 2.791 1.740 2.023 1.145
HIS266 NE22040 3.569 2.818 1.751 2.718 1.754 1.737 1.230
MET269 SD2069 3.703 3.181 1.366 2.426 2.000 1.785 0.393
MET295 SD2270 3.667 3.082 2.553 3.399 2.621 2.902 1.745
MET301 SD2319 3.895 3.339 2.036 3.015 2.459 2.455 1.109
MET302 SD2327 3.322 2.940 1.579 2.379 2.025 2.049 0.984
CYS305 SG2344 4.070 3.538 1.496 2.586 2.269 1.899 0.631
HIS309 NE22380 5.015 4.371 2.476 3.567 3.173 2.784 1.669
MET323 SD2490 3.923 3.356 3.490 4.220 3.343 3.798 2.753
MET325 SD2504 3.279 2.622 3.358 4.001 2.900 3.538 2.750
MET332 SD2563 3.840 3.150 2.869 3.750 2.813 3.153 2.023
CYS356 SG2758 2.522 1.958 2.633 3.153 2.120 2.795 2.218
MET373 SD2827 3.743 3.270 3.317 3.984 3.219 3.656 2.647
MET398 SD3022 4.586 4.333 1.577 2.130 2.768 1.851 1.865
HIS406 NE23099 4.990 4.869 2.384 2.412 3.332 2.372 2.993
MET413 SD3156 3.783 3.614 1.369 1.402 2.094 1.166 2.155
MET416 SD3181 4.434 4.127 2.125 2.346 2.669 1.843 2.663
MET425 SD3253 3.887 3.442 1.047 1.957 1.911 1.143 1.151
CYS213 HIS229 MET235 CYS241 MET259 HIS266 MET269
SG1626 NE21758 SD1798 SG1836 SD1978 NE22040 SD2069
HIS229 NE21758 1.013
MET235 SD1798 1.438 1.419
CYS241 SG1836 1.865 1.621 1.143
MET259 SD1978 2.206 2.590 1.609 1.454
HIS266 NE22040 2.762 3.311 2.158 2.353 0.969
MET269 SD2069 1.496 2.231 1.470 1.868 1.088 1.315
MET295 SD2270 1.717 1.960 1.754 1.120 1.232 2.135 1.489
MET301 SD2319 1.377 2.027 1.651 1.598 1.123 1.737 0.759
MET302 SD2327 0.890 1.376 0.899 1.238 1.340 1.973 0.884
CYS305 SG2344 1.733 2.571 1.864 2.301 1.384 1.350 0.437
HIS309 NE22380 2.567 3.472 2.903 3.129 1.992 1.737 1.434
MET323 SD2490 2.461 2.367 2.481 1.473 2.061 3.000 2.516
MET325 SD2504 2.834 2.651 2.362 1.251 1.843 2.759 2.611
MET332 SD2563 2.223 2.466 2.159 1.411 1.245 2.114 1.762
CYS356 SG2758 2.363 2.104 1.558 0.512 1.517 2.416 2.187
MET373 SD2827 2.165 1.964 2.222 1.252 2.099 3.057 2.432
MET398 SD3022 2.629 3.411 2.704 3.646 2.954 2.549 2.058
HIS406 NE23099 3.821 4.463 3.641 4.677 3.997 3.438 3.263
MET413 SD3156 3.234 3.739 2.654 3.656 3.013 2.501 2.508
MET416 SD3181 3.969 4.575 3.427 4.302 3.375 2.619 2.970
MET425 SD3253 2.563 3.264 2.197 2.964 1.997 1.425 1.422
MET295 MET301 MET302 CYS305 HIS309 MET323 MET325
SD2270 SD2319 SD2327 SG2344 NE22380 SD2490 SD2504
MET301 SD2319 0.843
MET302 SD2327 1.153 0.826
CYS305 SG2344 1.823 1.021 1.278
HIS309 NE22380 2.358 1.629 2.220 1.071
MET323 SD2490 1.027 1.850 2.065 2.846 3.269
MET325 SD2504 1.337 2.125 2.219 2.981 3.494 0.889
MET332 SD2563 0.521 1.148 1.615 2.047 2.401 0.950 1.164
CYS356 SG2758 1.310 1.903 1.687 2.608 3.355 1.423 0.901
MET373 SD2827 1.002 1.793 1.850 2.789 3.326 0.434 1.052
MET398 SD3022 3.515 2.742 2.562 1.824 2.320 4.532 4.607
HIS406 NE23099 4.718 3.991 3.728 3.064 3.498 5.725 5.686
MET413 SD3156 3.862 3.255 2.914 2.436 3.111 4.825 4.651
MET416 SD3181 4.368 3.723 3.569 2.799 3.175 5.345 5.142
MET425 SD3253 2.860 2.173 2.102 1.253 1.851 3.865 3.782
MET332 CYS356 MET373 MET398 HIS406 MET413 MET416
SD2563 SG2758 SD2827 SD3022 NE23099 SD3156 SD3181
CYS356 SG2758 1.419
MET373 SD2827 1.138 1.316
MET398 SD3022 3.819 4.015 4.383
HIS406 NE23099 5.008 5.010 5.566 1.329
MET413 SD3156 4.128 3.932 4.676 1.353 1.264
MET416 SD3181 4.543 4.516 5.264 1.756 1.359 0.992
MET425 SD3253 3.061 3.226 3.788 1.175 2.044 1.292 1.555
Select start terminus type for MET-1
0: MET1
1: NH3+
2: NH2
3: HYD1
4: 5TER
5: 5MET
6: 5PHO
7: 5POM
8: None
1
Start terminus MET-1: NH3+
Select end terminus type for ASP-437
0: COO-
1: COOH
2: CT2
3: CT1
4: HYD2
5: MET2
6: 3TER
7: None
0
End terminus ASP-437: COO-
Opening force field file D:\gmx2020.6_GPU/share/gromacs/top/charmm36.ff/aminoacids.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Now there are 427 residues with 6601 atoms
Chain time…
Making bonds…
Number of bonds was 6676, now 6676
Generating angles, dihedrals and pairs…
Before cleaning: 17410 pairs
Before cleaning: 17580 dihedrals
Keeping all generated dihedrals
Making cmap torsions…
There are 425 cmap torsion pairs
There are 17580 dihedrals, 1207 impropers, 12009 angles
17284 pairs, 6676 bonds and 0 virtual sites
Total mass 47879.341 a.m.u.
Total charge -15.000 e
Writing topology
Processing chain 3 ‘A’ (32 atoms, 1 residues)
Identified residue GTP500 as a starting terminus.
Identified residue GTP500 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Select start terminus type for GTP-500
0: NH3+
1: NH2
2: HYD1
3: MET1
4: 5TER
5: 5MET
6: 5PHO
7: 5POM
8: None
0
Start terminus GTP-500: NH3+
Select end terminus type for GTP-500
0: COO-
1: COOH
2: CT2
3: CT1
4: HYD2
5: MET2
6: 3TER
7: None
0
End terminus GTP-500: COO-
Program: gmx pdb2gmx, version 2020.6-MODIFIED
Source file: src\gromacs\gmxpreprocess\pdb2top.cpp (line 1079)
Fatal error:
atom N not found in buiding block 1GTP while combining tdb and rtp
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
PS C:\Users\Administrator\Desktop\weiguandanbai>