Hi Andras,
Thank you for your valuable suggestion, now I am able to generate a topology file using an updated version of GROMACS with CHARMm36 force field according to your explanation. Please let me know if you can reproduce the error by using version 5.1.4 just for my knowledge.
Thanks & Best Regards
Pooja singh
What if you input -f file is already a GROMACs .gro file, say you made it with CHARMM GUI and you want to run pdb2gmx on that *.gro file with the toplogy .top and inlcudes .itp files to make vsites. There is no TER in .gro files so for this input for example 1068 is last residue of Protein_chain_A in complex.gro.
1068ASN O117492 -4.744 -0.953 -1.574
1068ASN O217493 -4.522 -0.983 -1.601
1GLU N17494 -4.693 -0.509 4.976
running
gmx pdb2gmx -f complex.gro -p topol.top -o test.gro -vsite hydrogens
gives the canonical
Fatal error:
Atom O1 in residue ASN 1068 was not found in rtp entry ASN with 14 atoms
while sorting atoms.
Does recognition of chain terminators only work if input is in PDB format/is PDB file? And if so, how can you convert say a “multiple chain” .gro file back to a multiple chain PDB file?
The .gro format does not support any sort of chain identifiers, so pdb2gmx will fail for any input .gro file that has more than one chain. Use .pdb format in this instance, and make sure all chains are indicated by chain IDs or separated by TER.
Hi, I have been running into errors trying to create a topology file for an .pdb file that I have. I am using GROMACS 2018 on a server computer and the CHARMM36 2021 force field. I have also tried using older force field releases from 2020, 2019, and 2017, but all of these generate the same error.
gmx pdb2gmx -f equil_Piezo1_923.pdb -o equil_1bar_DV.pdb -p equil_1bar_DV.top -ff charmm36-jul2021
Program: gmx pdb2gmx, version 2018.1
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 753)
Fatal error:
Atom OT1 in residue LEU 141 was not found in rtp entry LEU with 19 atoms
while sorting atoms.
Looking at my original pdb file, this particular LEU has 20 atoms with OT1 and OT2 at the terminus.
Inside aminoacids.rpt LEU is supposed to only have 19 atoms with an O as the terminus.
Is there a way to reconcile this? The atomistic pdb does not appear to have missing atoms.
Thank you for any advice,
Kyrstyn
OT1 and OT2 refer to the carboxylate O atoms at the C-terminus. Your input coordinate file suggests that Leu141 is the C-terminal residue, but for some reason, pdb2gmx does not think it is. Please provide the full screen output of pdb2gmx so we can see what it is doing.
Thank you. I have attached the full screen output of pdb2gmx in the following file.
output.log (579.5 KB)
Warning: Residue POPC4681 in chain has different type ('Other') from
residue LEU1 ('Protein'). This chain lacks identifiers, which makes
it impossible to do strict classification of the start/end residues. Here we
need to guess this residue should not be part of the chain and instead
introduce a break, but that will be catastrophic if they should in fact be
linked. Please check your structure, and add POPC to residuetypes.dat
if this was not correct.
It appears you have a very complex, multi-component system that you’re trying to pass to pdb2gmx all at once. While this is supported, it requires you to carefully prepare the input file with appropriate chain identifiers or TER delimiters. I suspect you have not done this, hence why pdb2gmx is finding an internal residue when it should find a terminus, in the case of Leu141.
Thank you for pointing this out about the TER delimiters. I had to use editconf to create a pdb file from a .gro file, which is what I have available. Is there a better way to create a pdb file from a gro file to make sure that the chain identifiers are included?
If you are starting with a .gro file, you simply have to add all the appropriate delimiters yourself, since .gro format does not support this information.
Hi, I am facing this error during creating a topology file for protein.
Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 790)
Fatal error:
Atom OXT in residue SER 434 was not found in rtp entry SER with 11 atoms
while sorting atoms.
How can I solve it? Please help me.
Your problem is different than the one that started this thread, but in any case please provide the complete pdb2gmx terminal output, copied and pasted directly and including the command you gave.
ruhul@ruhul:~/MD/simulation$ gmx pdb2gmx -f protein_processed.pdb -ignh -o protein_processed.gro
:-) GROMACS - gmx pdb2gmx, 2021.4-Ubuntu-2021.4-2 (-:
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Carsten Kutzner Per Larsson Justin A. Lemkul
Viveca Lindahl Magnus Lundborg Erik Marklund
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and the project leaders:
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GROMACS: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/ruhul/MD/simulation
Command line:
gmx pdb2gmx -f protein_processed.pdb -ignh -o protein_processed.gro
Select the Force Field:
From current directory:
1: CHARMM all-atom force field
From ‘/usr/share/gromacs/top’:
2: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
3: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
4: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
5: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
6: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
7: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
8: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
9: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
10: GROMOS96 43a1 force field
11: GROMOS96 43a2 force field (improved alkane dihedrals)
12: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
13: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
15: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9)
16: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
1
Using the Charmm36-jul2022 force field in directory ./charmm36-jul2022.ff
Opening force field file ./charmm36-jul2022.ff/watermodels.dat
Select the Water Model:
1: TIP3P CHARMM-modified TIP3P water model (recommended over original TIP3P)
2: TIP3P_ORIGINAL Original TIP3P water model
3: SPC SPC water model
4: SPCE SPC/E water model
5: TIP5P TIP5P water model
6: TIP4P TIP4P water model
7: TIP4PEW TIP4P/Ew water model
8: None
1
going to rename ./charmm36-jul2022.ff/aminoacids.r2b
Opening force field file ./charmm36-jul2022.ff/aminoacids.r2b
going to rename ./charmm36-jul2022.ff/carb.r2b
Opening force field file ./charmm36-jul2022.ff/carb.r2b
going to rename ./charmm36-jul2022.ff/cgenff.r2b
Opening force field file ./charmm36-jul2022.ff/cgenff.r2b
going to rename ./charmm36-jul2022.ff/ethers.r2b
Opening force field file ./charmm36-jul2022.ff/ethers.r2b
going to rename ./charmm36-jul2022.ff/lipid.r2b
Opening force field file ./charmm36-jul2022.ff/lipid.r2b
going to rename ./charmm36-jul2022.ff/metals.r2b
Opening force field file ./charmm36-jul2022.ff/metals.r2b
going to rename ./charmm36-jul2022.ff/na.r2b
Opening force field file ./charmm36-jul2022.ff/na.r2b
going to rename ./charmm36-jul2022.ff/silicates.r2b
Opening force field file ./charmm36-jul2022.ff/silicates.r2b
going to rename ./charmm36-jul2022.ff/solvent.r2b
Opening force field file ./charmm36-jul2022.ff/solvent.r2b
Reading protein_processed.pdb…
WARNING: all CONECT records are ignored
Read 'D:\Megasync\Document\Research\Docking\RB Peptides\Docking\Antihypertensive\ACE\Final\MD simulation\ACE_YY_complex.pdbqt ', 4686 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 574 residues with 4686 atoms
chain #res #atoms
1 ‘A’ 574 4686
All occupancies are one
All occupancies are one
Opening force field file ./charmm36-jul2022.ff/atomtypes.atp
Reading residue database… (Charmm36-jul2022)
Opening force field file ./charmm36-jul2022.ff/aminoacids.rtp
Opening force field file ./charmm36-jul2022.ff/carb.rtp
Opening force field file ./charmm36-jul2022.ff/cgenff.rtp
Opening force field file ./charmm36-jul2022.ff/ethers.rtp
Opening force field file ./charmm36-jul2022.ff/lipid.rtp
Opening force field file ./charmm36-jul2022.ff/metals.rtp
Opening force field file ./charmm36-jul2022.ff/na.rtp
Opening force field file ./charmm36-jul2022.ff/silicates.rtp
Opening force field file ./charmm36-jul2022.ff/solvent.rtp
Opening force field file ./charmm36-jul2022.ff/aminoacids.hdb
Opening force field file ./charmm36-jul2022.ff/carb.hdb
Opening force field file ./charmm36-jul2022.ff/cgenff.hdb
Opening force field file ./charmm36-jul2022.ff/ethers.hdb
Opening force field file ./charmm36-jul2022.ff/lipid.hdb
Opening force field file ./charmm36-jul2022.ff/metals.hdb
Opening force field file ./charmm36-jul2022.ff/na.hdb
Opening force field file ./charmm36-jul2022.ff/silicates.hdb
Opening force field file ./charmm36-jul2022.ff/solvent.hdb
Opening force field file ./charmm36-jul2022.ff/aminoacids.n.tdb
Opening force field file ./charmm36-jul2022.ff/carb.n.tdb
Opening force field file ./charmm36-jul2022.ff/cgenff.n.tdb
Opening force field file ./charmm36-jul2022.ff/ethers.n.tdb
Opening force field file ./charmm36-jul2022.ff/lipid.n.tdb
Opening force field file ./charmm36-jul2022.ff/metals.n.tdb
Opening force field file ./charmm36-jul2022.ff/na.n.tdb
Opening force field file ./charmm36-jul2022.ff/silicates.n.tdb
Opening force field file ./charmm36-jul2022.ff/solvent.n.tdb
Opening force field file ./charmm36-jul2022.ff/aminoacids.c.tdb
Opening force field file ./charmm36-jul2022.ff/carb.c.tdb
Opening force field file ./charmm36-jul2022.ff/cgenff.c.tdb
Opening force field file ./charmm36-jul2022.ff/ethers.c.tdb
Opening force field file ./charmm36-jul2022.ff/lipid.c.tdb
Opening force field file ./charmm36-jul2022.ff/metals.c.tdb
Opening force field file ./charmm36-jul2022.ff/na.c.tdb
Opening force field file ./charmm36-jul2022.ff/silicates.c.tdb
Opening force field file ./charmm36-jul2022.ff/solvent.c.tdb
Processing chain 1 ‘A’ (4686 atoms, 574 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 885 donors and 857 acceptors were found.
There are 1153 hydrogen bonds
Will use HISE for residue 91
Will use HISE for residue 153
Will use HISE for residue 248
Will use HISE for residue 256
Will use HISE for residue 258
Will use HISE for residue 263
Will use HISE for residue 273
Will use HISE for residue 353
Will use HISD for residue 382
Will use HISD for residue 383
Will use HISE for residue 387
Will use HISE for residue 410
Will use HISD for residue 426
Will use HISE for residue 428
Will use HISD for residue 442
Will use HISE for residue 513
Will use HISE for residue 534
Will use HISE for residue 543
Will use HISE for residue 548
Will use HISE for residue 610
Identified residue ASP40 as a starting terminus.
Identified residue PRO617 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET86 HIS91 MET142 CYS152 HIS153 CYS158 MET169
SD391 NE2432 SD851 SG925 NE2935 SG966 SD1052
HIS91 NE2432 1.518
MET142 SD851 1.719 2.724
CYS152 SG925 3.387 4.410 2.180
HIS153 NE2935 4.077 4.941 2.704 0.887
CYS158 SG966 3.432 4.428 2.297 0.204 0.903
MET169 SD1052 3.816 4.467 2.275 1.597 1.158 1.681
MET223 SD1503 2.153 1.943 1.823 3.634 3.907 3.707 3.085
HIS248 NE21722 4.655 5.044 3.075 3.315 2.886 3.438 1.816
HIS256 NE21791 5.674 6.193 4.012 3.563 2.892 3.670 2.178
HIS258 NE21812 5.146 5.676 3.587 2.655 1.863 2.706 1.350
HIS263 NE21852 5.282 6.011 3.599 2.738 2.057 2.849 1.679
HIS273 NE21926 4.386 5.095 2.728 2.059 1.503 2.178 0.803
MET278 SD1961 3.393 4.083 1.835 1.489 1.314 1.595 0.441
MET299 SD2131 5.409 5.362 4.398 3.773 3.204 3.714 2.735
MET305 SD2175 4.285 4.291 3.385 2.964 2.612 2.903 2.123
MET315 SD2263 3.827 3.826 3.090 2.789 2.607 2.716 2.199
MET340 SD2469 2.565 2.853 2.220 2.232 2.551 2.155 2.420
CYS352 SG2562 2.750 3.244 1.936 1.663 1.901 1.611 1.741
HIS353 NE22572 2.537 2.840 1.516 2.255 2.401 2.292 1.693
CYS370 SG2716 2.784 3.189 2.069 1.851 2.064 1.788 1.885
HIS382 NE22807 3.937 3.612 3.302 3.550 3.377 3.514 2.680
HIS383 NE22817 2.920 2.808 2.155 3.001 3.028 3.023 2.192
MET385 SD2833 3.272 2.888 2.953 3.406 3.447 3.360 2.883
HIS387 NE22848 2.698 2.484 2.133 3.137 3.244 3.155 2.465
MET392 SD2895 3.187 2.433 3.260 4.055 4.196 4.014 3.618
HIS410 NE23038 2.576 2.013 2.408 3.691 3.876 3.709 3.115
HIS426 NE23152 4.579 4.203 3.889 3.986 3.695 3.945 2.995
HIS428 NE23170 5.658 5.412 4.778 4.394 3.884 4.336 3.324
HIS442 NE23248 5.906 5.804 4.750 4.389 3.754 4.377 3.033
MET448 SD3298 4.939 5.049 3.569 3.558 3.014 3.613 1.991
MET450 SD3315 4.465 4.340 3.390 3.584 3.196 3.600 2.238
CYS496 SG3720 4.415 5.063 2.722 2.726 2.348 2.876 1.462
HIS513 NE23852 2.506 2.771 1.422 2.504 2.644 2.567 1.818
HIS534 NE24037 4.613 4.197 3.780 4.326 4.030 4.342 3.052
CYS538 SG4065 4.744 4.210 4.022 4.638 4.367 4.649 3.405
HIS543 NE24098 5.303 4.802 4.488 4.941 4.575 4.950 3.618
HIS548 NE24134 5.357 5.090 4.301 4.516 4.042 4.535 3.077
CYS550 SG4149 4.861 4.332 4.135 4.664 4.370 4.667 3.435
MET566 SD4271 3.352 2.615 3.136 4.183 4.233 4.184 3.423
MET578 SD4370 3.923 3.320 3.367 4.642 4.583 4.695 3.543
MET587 SD4438 3.537 3.191 2.800 4.215 4.200 4.295 3.136
MET592 SD4468 4.154 4.006 3.061 3.866 3.618 3.935 2.496
HIS610 NE24630 6.092 6.339 4.558 4.278 3.582 4.353 2.737
MET223 HIS248 HIS256 HIS258 HIS263 HIS273 MET278
SD1503 NE21722 NE21791 NE21812 NE21852 NE21926 SD1961
HIS248 NE21722 3.196
HIS256 NE21791 4.427 1.309
HIS258 NE21812 4.145 1.774 1.315
HIS263 NE21852 4.422 1.769 1.043 1.069
HIS273 NE21926 3.566 1.477 1.523 1.059 0.926
MET278 SD1961 2.729 1.906 2.470 1.773 1.994 1.073
MET299 SD2131 4.201 3.242 3.367 2.429 3.490 3.125 2.987
MET305 SD2175 3.263 3.008 3.450 2.429 3.378 2.745 2.238
MET315 SD2263 2.989 3.252 3.807 2.779 3.645 2.916 2.216
MET340 SD2469 2.561 3.781 4.490 3.514 4.090 3.218 2.207
CYS352 SG2562 2.564 3.216 3.854 2.881 3.406 2.536 1.538
HIS353 NE22572 1.628 2.571 3.508 2.841 3.288 2.378 1.387
CYS370 SG2716 2.563 3.314 3.965 2.979 3.549 2.685 1.699
HIS382 NE22807 2.626 3.188 3.950 3.176 4.027 3.308 2.652
HIS383 NE22817 1.478 2.649 3.674 3.089 3.662 2.814 1.979
MET385 SD2833 2.292 3.632 4.485 3.666 4.423 3.604 2.745
HIS387 NE22848 1.295 2.947 3.998 3.415 3.968 3.103 2.218
MET392 SD2895 2.251 4.224 5.186 4.453 5.167 4.327 3.427
HIS410 NE23038 1.100 3.463 4.586 4.071 4.598 3.734 2.842
HIS426 NE23152 3.174 3.334 3.973 3.225 4.157 3.543 3.047
HIS428 NE23170 4.303 3.612 3.854 3.062 4.104 3.723 3.528
HIS442 NE23248 4.359 2.849 2.926 2.427 3.388 3.191 3.302
MET448 SD3298 3.333 1.330 1.839 1.665 2.346 2.014 2.189
MET450 SD3315 2.827 2.132 2.854 2.357 3.166 2.604 2.320
CYS496 SG3720 3.344 0.881 1.373 1.673 1.279 0.917 1.527
HIS513 NE23852 1.314 2.398 3.448 2.935 3.305 2.408 1.489
HIS534 NE24037 2.760 2.713 3.571 3.233 3.990 3.422 3.061
CYS538 SG4065 2.871 3.058 3.925 3.596 4.361 3.790 3.401
HIS543 NE24098 3.421 3.136 3.855 3.588 4.387 3.924 3.679
HIS548 NE24134 3.537 2.505 3.069 2.844 3.641 3.275 3.211
CYS550 SG4149 3.030 3.137 3.948 3.580 4.381 3.826 3.451
MET566 SD4271 1.770 3.612 4.682 4.166 4.821 4.020 3.235
MET578 SD4370 1.820 3.024 4.210 4.091 4.587 3.906 3.376
MET587 SD4438 1.396 2.555 3.822 3.790 4.139 3.441 2.923
MET592 SD4468 2.209 1.767 2.888 2.826 3.313 2.722 2.438
HIS610 NE24630 4.536 1.632 1.170 1.778 2.102 2.342 3.031
MET299 MET305 MET315 MET340 CYS352 HIS353 CYS370
SD2131 SD2175 SD2263 SD2469 SG2562 NE22572 SG2716
MET305 SD2175 1.145
MET315 SD2263 1.682 0.565
MET340 SD2469 3.130 1.999 1.474
CYS352 SG2562 2.898 1.807 1.411 0.695
HIS353 NE22572 2.977 1.938 1.660 1.367 1.065
CYS370 SG2716 2.825 1.713 1.276 0.544 0.204 1.099
HIS382 NE22807 1.838 1.069 0.996 2.041 2.077 1.800 1.943
HIS383 NE22817 2.744 1.789 1.567 1.730 1.637 0.794 1.584
MET385 SD2833 2.552 1.568 1.161 1.484 1.767 1.591 1.598
HIS387 NE22848 3.000 2.015 1.722 1.679 1.708 0.908 1.639
MET392 SD2895 3.274 2.375 1.980 1.975 2.404 2.125 2.238
HIS410 NE23038 3.520 2.570 2.246 2.048 2.237 1.496 2.151
HIS426 NE23152 1.475 1.164 1.339 2.613 2.614 2.379 2.485
HIS428 NE23170 0.738 1.527 1.983 3.452 3.330 3.292 3.228
HIS442 NE23248 1.151 1.987 2.529 3.927 3.621 3.395 3.577
MET448 SD3298 2.040 2.074 2.468 3.462 3.004 2.486 3.029
MET450 SD3315 1.653 1.405 1.722 2.826 2.550 2.021 2.508
CYS496 SG3720 3.604 3.234 3.402 3.671 3.035 2.557 3.177
HIS513 NE23852 3.187 2.212 1.988 1.748 1.470 0.417 1.512
HIS534 NE24037 2.207 2.005 2.206 3.217 3.098 2.439 3.023
CYS538 SG4065 2.411 2.238 2.406 3.396 3.342 2.687 3.252
HIS543 NE24098 2.301 2.415 2.694 3.836 3.735 3.138 3.650
HIS548 NE24134 1.909 2.172 2.569 3.783 3.537 2.987 3.488
CYS550 SG4149 2.269 2.161 2.355 3.414 3.363 2.764 3.268
MET566 SD4271 3.202 2.423 2.193 2.444 2.648 1.987 2.529
MET578 SD4370 3.583 3.052 3.023 3.433 3.403 2.455 3.349
MET587 SD4438 3.743 3.120 3.074 3.300 3.168 2.128 3.157
MET592 SD4468 2.802 2.410 2.559 3.222 2.937 2.043 2.934
HIS610 NE24630 2.888 3.255 3.709 4.697 4.154 3.723 4.213
HIS382 HIS383 MET385 HIS387 MET392 HIS410 HIS426
NE22807 NE22817 SD2833 NE22848 SD2895 NE23038 NE23152
HIS383 NE22817 1.251
MET385 SD2833 0.850 1.157
HIS387 NE22848 1.378 0.340 1.081
MET392 SD2895 1.499 1.622 0.832 1.395
HIS410 NE23038 1.751 0.985 1.304 0.671 1.169
HIS426 NE23152 0.643 1.824 1.434 1.979 1.971 2.312
HIS428 NE23170 1.803 2.891 2.569 3.109 3.162 3.524 1.241
HIS442 NE23248 2.331 3.054 3.165 3.344 3.805 3.826 1.887
MET448 SD3298 2.289 2.294 2.958 2.625 3.606 3.166 2.232
MET450 SD3315 1.269 1.577 2.002 1.873 2.613 2.363 1.228
CYS496 SG3720 3.559 2.886 3.869 3.162 4.497 3.715 3.800
HIS513 NE23852 1.960 0.779 1.799 0.884 2.238 1.403 2.519
HIS534 NE24037 1.364 1.757 2.039 1.944 2.390 2.194 1.232
CYS538 SG4065 1.485 1.958 2.109 2.094 2.346 2.242 1.306
HIS543 NE24098 1.859 2.459 2.584 2.631 2.874 2.827 1.496
HIS548 NE24134 1.974 2.460 2.776 2.718 3.257 3.080 1.637
CYS550 SG4149 1.446 2.047 2.116 2.191 2.380 2.361 1.184
MET566 SD4271 1.406 1.258 1.197 1.086 0.973 0.798 1.820
MET578 SD4370 2.191 1.767 2.369 1.766 2.340 1.634 2.410
MET587 SD4438 2.424 1.628 2.540 1.660 2.622 1.644 2.745
MET592 SD4468 1.990 1.574 2.452 1.811 2.843 2.145 2.141
HIS610 NE24630 3.636 3.642 4.327 3.974 4.989 4.512 3.488
HIS428 HIS442 MET448 MET450 CYS496 HIS513 HIS534
NE23170 NE23248 SD3298 SD3315 SG3720 NE23852 NE24037
HIS442 NE23248 1.163
MET448 SD3298 2.321 1.545
MET450 SD3315 1.745 1.532 1.064
CYS496 SG3720 4.093 3.428 1.988 2.694
HIS513 NE23852 3.464 3.475 2.437 2.030 2.432
HIS534 NE24037 1.990 1.953 1.752 0.899 3.372 2.372
CYS538 SG4065 2.091 2.161 2.105 1.255 3.729 2.617 0.371
HIS543 NE24098 1.899 1.824 2.055 1.386 3.868 3.081 0.711
HIS548 NE24134 1.724 1.197 1.312 0.994 3.244 2.944 0.958
CYS550 SG4149 1.911 2.031 2.115 1.247 3.804 2.721 0.439
MET566 SD4271 3.053 3.440 3.049 2.105 4.014 1.934 1.698
MET578 SD4370 3.426 3.378 2.674 2.054 3.609 2.197 1.478
MET587 SD4438 3.728 3.550 2.529 2.126 3.053 1.784 1.847
MET592 SD4468 2.850 2.468 1.394 1.154 2.434 1.818 1.176
HIS610 NE24630 3.204 2.111 1.384 2.411 2.198 3.656 2.984
CYS538 HIS543 HIS548 CYS550 MET566 MET578 MET587
SG4065 NE24098 NE24134 SG4149 SD4271 SD4370 SD4438
HIS543 NE24098 0.593
HIS548 NE24134 1.160 0.835
CYS550 SG4149 0.203 0.497 1.100
MET566 SD4271 1.642 2.227 2.643 1.743
MET578 SD4370 1.443 1.925 2.278 1.643 1.368
MET587 SD4438 1.947 2.399 2.519 2.141 1.727 0.754
MET592 SD4468 1.453 1.724 1.520 1.594 2.044 1.332 1.156
HIS610 NE24630 3.294 3.074 2.260 3.289 4.408 3.845 3.645
MET592
SD4468
HIS610 NE24630 2.564
Linking CYS-152 SG-925 and CYS-158 SG-966…
Linking CYS-352 SG-2562 and CYS-370 SG-2716…
Linking CYS-538 SG-4065 and CYS-550 SG-4149…
Start terminus ASP-40: NH3+
End terminus PRO-617: COO-
Opening force field file ./charmm36-jul2022.ff/aminoacids.arn
Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/pdb2gmx.cpp (line 790)
Fatal error:
Atom OXT in residue SER 434 was not found in rtp entry SER with 11 atoms
while sorting atoms.
.
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
You have a gap in the chain, meaning there are missing residues and false termini in residues 434 and 439:
ATOM 3907 N SER A 434 64.099 23.522 31.944 1.00 0.00 N
ATOM 3908 CA SER A 434 65.416 23.262 31.311 1.00 0.00 C
ATOM 3909 C SER A 434 65.679 24.163 30.097 1.00 0.00 C
ATOM 3910 O SER A 434 66.214 25.277 30.281 1.00 0.00 O
ATOM 3911 CB SER A 434 65.534 21.781 30.934 1.00 0.00 C
ATOM 3912 OG SER A 434 64.417 21.381 30.127 1.00 0.00 O
ATOM 3913 H SER A 434 63.313 23.210 31.412 1.00 0.00 H
ATOM 3914 HG SER A 434 64.567 20.451 29.786 1.00 0.00 H
ATOM 3915 OXT SER A 434 65.204 23.790 29.011 1.00 0.00 O
ATOM 3916 N SER A 439 64.493 32.707 21.995 1.00 0.00 N
ATOM 3917 CA SER A 439 63.945 31.893 20.883 1.00 0.00 C
ATOM 3918 C SER A 439 62.467 32.226 20.609 1.00 0.00 C
ATOM 3919 O SER A 439 61.613 32.125 21.492 1.00 0.00 O
ATOM 3920 CB SER A 439 64.090 30.389 21.178 1.00 0.00 C
ATOM 3921 OG SER A 439 63.479 29.572 20.164 1.00 0.00 O
ATOM 3922 H1 SER A 439 63.787 33.327 22.340 1.00 0.00 H
ATOM 3923 HG SER A 439 63.812 28.626 20.264 1.00 0.00 H
ATOM 3924 H2 SER A 439 64.827 32.143 22.737 1.00 0.00 H
ATOM 3925 H3 SER A 439 65.278 33.229 21.696 1.00 0.00 H
pdb2gmx is finding OXT (which corresponds to a C-terminal acidic oxygen) in a non-terminal residue, so it triggers an error. Then the presence of H[123] in residue 439 means that is a new N-terminus, but there is a gap from residues 435-438 that means you have an incomplete structure.
By default, this protein (PDB ID:1o86) structure has to miss these residues (435 - 438). Please check the raw file of that protein which I have attached here.
You can also check the structure from this link (RCSB PDB - 1O86: Crystal Structure of Human Angiotensin Converting Enzyme in complex with lisinopril.).
I don’t understand what should I do.
protein(PDB:1o86).dat (460.7 KB)
You can’t simulate something reasonably with gaps in the chains. You need to model in the missing residues with software like Modeller or Rosetta.
Ok sir. Thank you for your kind information.
But there is one more thing if I replace the OXT with O in residue SER 434, then it creates the topology file without any fatal error. So what’s your opinion about this?
Is this the right way to solve the error?
You will have an artificially strained bond that will never minimize properly, and you will still be missing the residues that should be in between 434 and 439. The outcomes of the simulations will be fictitious. Build in the missing residues.
Ok sir. I have another question. I want to perform MD simulation after molecular docking(protein-peptide docking). I already performed docking with this protein(1o86) without building missing residues.
After building missing residues, should I again perform docking? Then docked complex will use for MD simulation?
If the missing residues might affect the docked pose, they need to be there before you try to dock anything to it. If they are far away, building them after docking is probably fine.