GROMACS version: 2022.4-Colvars_2023_01_19-dev
GROMACS modification: No
Hi there, I occurred a fatal error showing “Fatal error:
atom C2 not found in building block 465MET while combining tdb and rtp”
However, 465MET is not the terminal of the protein chain, and I have no idea what to define the C2 atom of MET.
I chose the force field “CHARMM36” [charmm36-jul2022.ff.tgz].
Down here are the error report in terminal code, and the MET defination in aminoacid.rtp in the charmm36 force field folder.
Any suggestions could work, I’ll be so appreciate to get help and solve this problem.
Terminal codeline:
:-) GROMACS - gmx pdb2gmx, 2022.4-Colvars_2023_09_19-dev (-:
Executable: /opt/gromacs-colvars/bin/gmx
Data prefix: /opt/gromacs-colvars
Working dir: /home/pereira/Desktop/3733 docking/GROMACS-Protein-Ligand-main
Command line:
gmx pdb2gmx -f REC.pdb -ignh
Select the Force Field:
From current directory:
1: CHARMM all-atom force field
From ‘/opt/gromacs-colvars/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 REC.pdb…
WARNING: all CONECT records are ignored
Read ‘’, 3738 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
Chain identifier ‘A’ is used in two non-sequential blocks. They will be treated as separate chains unless you reorder your file.
There are 2 chains and 0 blocks of water and 467 residues with 3738 atoms
chain #res #atoms
1 ‘A’ 465 3736
2 ‘A’ 2 2
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
Back Off! I just backed up topol.top to ./#topol.top.7#
Processing chain 1 ‘A’ (3736 atoms, 465 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 703 donors and 704 acceptors were found.
There are 934 hydrogen bonds
Will use HISE for residue 205
Will use HISE for residue 244
Will use HISE for residue 296
Will use HISE for residue 298
Will use HISD for residue 304
Will use HISD for residue 352
Will use HISE for residue 427
Will use HISH for residue 438
Will use HISE for residue 463
Will use HISE for residue 474
Will use HISD for residue 481
Identified residue GLY23 as a starting terminus.
Identified residue MET498 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
CYS77 MET107 MET134 CYS139 MET170 MET191 MET195
SG448 SD690 SD904 SG950 SD1103 SD1268 SD1301
MET107 SD690 1.781
MET134 SD904 2.949 1.391
CYS139 SG950 2.199 0.506 1.380
MET170 SD1103 4.110 3.359 3.753 3.376
MET191 SD1268 3.543 3.644 4.327 3.894 1.872
MET195 SD1301 3.319 3.559 4.158 3.887 2.373 0.764
HIS205 NE21398 4.279 3.572 3.803 3.651 0.706 1.763 2.117
CYS208 SG1425 4.078 3.665 4.100 3.803 0.940 1.118 1.601
CYS221 SG1529 3.572 3.557 4.576 3.622 2.070 1.980 2.617
CYS240 SG1676 2.401 3.235 4.166 3.621 3.120 1.598 1.305
HIS244 NE21705 1.350 1.894 2.941 2.296 2.914 2.208 2.022
HIS296 NE22129 3.825 4.458 5.436 4.724 3.092 1.540 1.880
HIS298 NE22150 3.135 3.834 4.899 4.106 2.976 1.561 1.835
HIS304 NE22200 1.227 1.508 2.675 1.878 2.886 2.473 2.383
MET309 SD2239 1.322 1.280 2.566 1.564 2.895 2.741 2.748
MET327 SD2384 3.292 2.705 3.295 2.799 0.829 1.499 1.901
CYS343 SG2524 2.918 3.983 5.247 4.244 3.933 2.770 2.953
MET351 SD2583 1.867 3.028 4.313 3.328 3.714 2.731 2.767
HIS352 NE22594 1.354 2.168 3.372 2.514 3.088 2.323 2.268
MET381 SD2816 2.270 2.541 3.835 2.641 2.961 2.750 3.054
CYS382 SG2823 1.553 2.103 3.484 2.268 3.497 3.206 3.329
CYS404 SG2992 1.451 2.649 4.018 2.890 4.231 3.624 3.644
HIS427 NE23183 0.969 2.041 3.327 2.384 3.487 2.830 2.759
HIS438 NE23269 1.549 3.202 4.459 3.556 4.700 3.692 3.543
CYS442 SG3295 1.605 3.127 4.374 3.489 4.268 3.179 3.050
CYS452 SG3371 1.384 1.723 2.506 2.197 3.189 2.583 2.226
MET455 SD3395 1.167 1.990 2.739 2.493 3.847 3.111 2.678
HIS463 NE23458 3.066 4.115 5.006 4.524 3.858 2.095 1.722
HIS474 NE23549 2.965 4.114 4.999 4.543 4.103 2.379 1.948
HIS481 NE23605 2.366 2.475 2.837 2.905 3.058 2.296 1.739
MET487 SD3650 1.543 1.170 1.960 1.615 2.929 2.727 2.495
MET498 SD3732 1.611 1.424 1.983 1.896 3.223 2.897 2.552
HIS205 CYS208 CYS221 CYS240 HIS244 HIS296 HIS298
NE21398 SG1425 SG1529 SG1676 NE21705 NE22129 NE22150
CYS208 SG1425 0.694
CYS221 SG1529 2.581 2.172
CYS240 SG1676 3.101 2.589 2.543
HIS244 NE21705 3.022 2.757 2.586 1.353
HIS296 NE22129 3.181 2.503 1.985 1.706 2.748
HIS298 NE22150 3.142 2.523 1.703 1.271 2.129 0.731
HIS304 NE22200 3.077 2.883 2.551 1.781 0.470 3.030 2.381
MET309 SD2239 3.176 3.036 2.503 2.186 0.937 3.274 2.609
MET327 SD2384 1.145 1.069 1.756 2.414 2.088 2.694 2.421
CYS343 SG2524 4.214 3.658 2.240 1.940 2.439 1.789 1.256
MET351 SD2583 3.979 3.533 2.375 1.618 1.579 2.323 1.612
HIS352 NE22594 3.296 2.960 2.318 1.359 0.607 2.531 1.837
MET381 SD2816 3.431 3.134 1.595 2.391 1.829 2.730 2.071
CYS382 SG2823 3.893 3.645 2.411 2.483 1.620 3.251 2.533
CYS404 SG2992 4.569 4.249 2.989 2.552 1.926 3.403 2.680
HIS427 NE23183 3.726 3.431 2.653 1.788 0.907 2.962 2.247
HIS438 NE23269 4.912 4.513 3.519 2.281 2.052 3.319 2.657
CYS442 SG3295 4.463 4.033 3.092 1.782 1.719 2.801 2.138
CYS452 SG3371 3.179 3.021 3.249 1.776 0.750 3.331 2.776
MET455 SD3395 3.822 3.643 3.773 2.032 1.187 3.690 3.119
HIS463 NE23458 3.763 3.187 3.192 0.938 2.231 1.738 1.588
HIS474 NE23549 4.001 3.451 3.451 1.079 2.255 2.061 1.862
HIS481 NE23605 2.824 2.682 3.550 1.834 1.485 3.317 2.945
MET487 SD3650 2.981 2.942 3.176 2.225 1.005 3.612 3.047
MET498 SD3732 3.192 3.154 3.546 2.295 1.211 3.799 3.259
HIS304 MET309 MET327 CYS343 MET351 HIS352 MET381
NE22200 SD2239 SD2384 SG2524 SD2583 NE22594 SD2816
MET309 SD2239 0.473
MET327 SD2384 2.066 2.108
CYS343 SG2524 2.585 2.713 3.301
MET351 SD2583 1.672 1.806 2.957 1.054
HIS352 NE22594 0.699 0.967 2.271 1.908 1.001
MET381 SD2816 1.611 1.405 2.303 1.887 1.412 1.375
CYS382 SG2823 1.324 1.072 2.755 2.164 1.327 1.183 0.848
CYS404 SG2992 1.778 1.695 3.458 1.981 1.115 1.427 1.509
HIS427 NE23183 0.817 0.937 2.670 2.060 1.027 0.509 1.419
HIS438 NE23269 2.127 2.267 3.897 1.930 1.164 1.643 2.305
CYS442 SG3295 1.863 2.061 3.475 1.536 0.735 1.275 2.037
CYS452 SG3371 0.924 1.320 2.406 3.135 2.245 1.320 2.513
MET455 SD3395 1.356 1.712 3.059 3.302 2.364 1.606 2.876
HIS463 NE23458 2.671 3.083 3.234 2.144 2.137 2.191 3.164
HIS474 NE23549 2.700 3.124 3.450 2.270 2.174 2.230 3.290
HIS481 NE23605 1.782 2.187 2.403 3.617 2.918 2.060 3.232
MET487 SD3650 0.885 1.084 2.177 3.417 2.514 1.525 2.423
MET498 SD3732 1.216 1.477 2.493 3.643 2.732 1.773 2.811
CYS382 CYS404 HIS427 HIS438 CYS442 CYS452 MET455
SG2823 SG2992 NE23183 NE23269 SG3295 SG3371 SD3395
CYS404 SG2992 0.867
HIS427 NE23183 0.917 1.022
HIS438 NE23269 1.791 1.054 1.349
CYS442 SG3295 1.677 1.139 1.130 0.531
CYS452 SG3371 2.187 2.438 1.453 2.448 2.207
MET455 SD3395 2.397 2.433 1.584 2.244 2.114 0.660
HIS463 NE23458 3.251 3.137 2.541 2.598 2.138 2.548 2.644
HIS474 NE23549 3.292 3.109 2.531 2.478 2.058 2.510 2.522
HIS481 NE23605 3.084 3.352 2.343 3.228 2.910 1.015 1.350
MET487 SD3650 2.117 2.553 1.616 2.799 2.586 0.637 1.148
MET498 SD3732 2.458 2.789 1.849 2.894 2.702 0.556 0.910
HIS463 HIS474 HIS481 MET487
NE23458 NE23549 NE23605 SD3650
HIS474 NE23549 0.340
HIS481 NE23605 2.441 2.430
MET487 SD3650 3.075 3.076 1.336
MET498 SD3732 3.068 3.032 1.113 0.444
Start terminus GLY-23: GLY-NH3+
End terminus MET-498: MET2
Program: gmx pdb2gmx, version 2022.4-Colvars_2023_09_19-dev
Source file: src/gromacs/gmxpreprocess/pdb2top.cpp (line 1132)
Fatal error:
atom C2 not found in buiding block 465MET 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
MET defination in CHARMM36 ff:
[ MET ]
;
[ atoms ]
N NH1 -0.4700 1
HN H 0.3100 1
CA CT1 0.0700 1
HA HB1 0.0900 1
CB CT2 -0.1800 2
HB1 HA2 0.0900 2
HB2 HA2 0.0900 2
CG CT2 -0.1400 3
HG1 HA2 0.0900 3
HG2 HA2 0.0900 3
SD S -0.0900 3
CE CT3 -0.2200 3
HE1 HA3 0.0900 3
HE2 HA3 0.0900 3
HE3 HA3 0.0900 3
C C 0.5100 4
O O -0.5100 4
[ bonds ]
CB CA
CG CB
SD CG
CE SD
N HN
N CA
C CA
C +N
CA HA
CB HB1
CB HB2
CG HG1
CG HG2
CE HE1
CE HE2
CE HE3
O C
[ impropers ]
N -C CA HN
C CA +N O
[ cmap ]
-C N CA C +N