# Fatal Error atom C2 not found in building block 465MET while combining tdb and rtp **URL:** \ **Category:** User discussions\ **Tags:** pdb2gmx\ **Created:** [January 25, 2024, 1:43pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-c2-not-found-in-building-block-465met-while-combining-tdb-and-rtp/8139 "2024-01-25T13:43:06Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![AuxenceH](https://avatars.discourse-cdn.com/v4/letter/a/a9adbd/32.png) [@AuxenceH](https://gromacs.bioexcel.eu/u/AuxenceH)\ **Post date:** [January 25, 2024, 1:43pm UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-c2-not-found-in-building-block-465met-while-combining-tdb-and-rtp/8139/1 "2024-01-25T13:43:06Z")
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](http://www.gromacs.org/Documentation/Errors) 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 ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 28, 2024, 3:08am UTC](https://gromacs.bioexcel.eu/t/fatal-error-atom-c2-not-found-in-building-block-465met-while-combining-tdb-and-rtp/8139/2 "2024-01-28T03:08:55Z")
Interactively select termini.