GROMACS version: gmx, version 2020.1-Ubuntu-2020.1-1
GROMACS modification: Yes/No
For the command line:
gmx pdb2gmx -f d4_clean.pdb -o d4_processed.gro -water spce
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)
Where I select the force field 1, charmm36 version jul 2022
The console give me this error:
Using the Charmm36-jul2022 force field in directory ./charmm36-jul2022.ff
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 d4_clean.pdb…
Read ‘’, 1310 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 166 residues with 1310 atoms
chain #res #atoms
1 ‘A’ 166 1310
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
Back Off! I just backed up topol.top to ./#topol.top.7#
Processing chain 1 ‘A’ (1310 atoms, 166 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 254 donors and 238 acceptors were found.
There are 356 hydrogen bonds
Will use HISE for residue 9
Will use HISE for residue 24
Will use HISE for residue 105
Will use HISE for residue 126
Identified residue LEU1 as a starting terminus.
Identified residue MET166 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET6 HIS9 MET19 HIS24 CYS41 MET46 MET51
SD44 NE271 SD146 NE2186 SG322 SD357 SD394
HIS9 NE271 1.034
MET19 SD146 1.580 1.277
HIS24 NE2186 0.390 0.856 1.289
CYS41 SG322 1.867 1.669 0.400 1.599
MET46 SD357 2.032 2.300 1.778 1.744 1.819
MET51 SD394 1.546 0.937 1.350 1.200 1.712 1.808
CYS52 SG401 1.928 1.531 1.894 1.600 2.209 1.734 0.663
CYS60 SG466 2.001 1.720 0.611 1.659 0.574 1.492 1.444
CYS73 SG566 1.916 1.737 0.632 1.581 0.576 1.343 1.475
CYS75 SG586 2.041 1.815 0.539 1.757 0.202 1.808 1.773
MET83 SD650 1.931 1.170 1.192 1.575 1.510 1.995 0.577
CYS87 SG680 2.004 1.685 2.052 1.690 2.358 1.725 0.849
HIS105 NE2827 5.326 5.050 4.905 4.991 5.014 3.858 4.117
MET108 SD844 5.893 5.584 5.447 5.558 5.555 4.441 4.649
MET118 SD926 7.966 7.750 7.714 7.667 7.833 6.531 6.836
HIS126 NE2990 8.126 7.986 7.881 7.831 7.974 6.583 7.074
MET147 SD1156 9.804 9.715 9.456 9.504 9.494 8.090 8.798
MET150 SD1181 10.414 10.311 10.103 10.118 10.154 8.747 9.394
MET165 SD1300 9.213 9.109 8.884 8.913 8.934 7.534 8.192
MET166 SD1308 8.725 8.660 8.501 8.440 8.572 7.104 7.757
CYS52 CYS60 CYS73 CYS75 MET83 CYS87 HIS105
SG401 SG466 SG566 SG586 SD650 SG680 NE2827
CYS60 SG466 1.828
CYS73 SG566 1.837 0.190
CYS75 SG586 2.239 0.483 0.513
MET83 SD650 1.047 1.203 1.305 1.528
CYS87 SG680 0.199 1.968 1.964 2.386 1.242
HIS105 NE2827 3.550 4.444 4.459 4.915 4.130 3.438
MET108 SD844 4.087 4.982 5.006 5.450 4.642 3.979 0.588
MET118 SD926 6.221 7.266 7.271 7.737 6.902 6.083 2.832
HIS126 NE2990 6.459 7.413 7.403 7.875 7.153 6.316 3.058
MET147 SD1156 8.211 8.941 8.924 9.376 8.842 8.075 4.765
MET150 SD1181 8.794 9.597 9.583 10.040 9.446 8.654 5.338
MET165 SD1300 7.599 8.378 8.363 8.820 8.242 7.462 4.151
MET166 SD1308 7.144 8.021 7.997 8.471 7.851 6.996 3.800
MET108 MET118 HIS126 MET147 MET150 MET165
SD844 SD926 NE2990 SD1156 SD1181 SD1300
MET118 SD926 2.351
HIS126 NE2990 2.638 0.730
MET147 SD1156 4.349 2.542 1.978
MET150 SD1181 4.893 2.862 2.396 0.749
MET165 SD1300 3.733 1.930 1.343 0.644 1.221
MET166 SD1308 3.429 1.607 0.915 1.282 1.734 0.746
Linking CYS-41 SG-322 and CYS-75 SG-586…
Linking CYS-52 SG-401 and CYS-87 SG-680…
Linking CYS-60 SG-466 and CYS-73 SG-566…
Start terminus LEU-1: NH3+
End terminus MET-166: MET2
Program: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1079)
Fatal error:
atom C2 not found in buiding block 166MET 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
I have to clarify that 166MET is the terminal position of my protein.
If anyone has any idea how to fix this error I would appreciate help.