# Zinc problem while running pdb2gmx **URL:** \ **Category:** User discussions\ **Created:** [November 8, 2025, 11:21pm UTC](https://gromacs.bioexcel.eu/t/zinc-problem-while-running-pdb2gmx/12885 "2025-11-08T23:21:18Z")\ **Posts on this page:** 1\ **Page:** 1
**Author:** ![hcps-leej9](https://avatars.discourse-cdn.com/v4/letter/h/ebca7d/32.png) [@hcps-leej9](https://gromacs.bioexcel.eu/u/hcps-leej9)\ **Post date:** [November 8, 2025, 11:21pm UTC](https://gromacs.bioexcel.eu/t/zinc-problem-while-running-pdb2gmx/12885/1 "2025-11-08T23:21:18Z")
GROMACS version: 2025.3-Homebrew GROMACS modification: Yes/ **No** Hi, I’m trying to run gmx pdb2gmx on a protein–zinc complex using the CHARMM27 force field, but I keep getting this error: My ultimate goal is to run MD with restraints on ZN and 3 HIS coordinating ZN (266,268,278) without any MCPB parameter or something like that ```auto Fatal error: Residue 'ZN' not found in residue topology database ``` this is the part of pdb that contains zinc ion ```auto ATOM 2968 C ASP A 315 -36.797 4.375 -8.741 1.00 15.00 A C ATOM 2969 O ASP A 315 -36.098 3.398 -8.434 1.00 15.00 A O TER HETATM 2970 ZN ZN Z1001 -37.232 -1.978 -4.906 1.00 15.00 Z ZN TER ATOM 2971 N MET B 1 17.112 -21.651 21.381 1.00 15.00 B N ATOM 2972 HN MET B 1 16.246 -21.280 21.658 1.00 15.00 B H ``` while executing i got ```auto MacBookPro GROMACS % gmx pdb2gmx -f complex.pdb -o complex_processed.gro -p topol.top -i posre.itp -water tip3p -ff charmm27 -ignh -merge no :-) GROMACS - gmx pdb2gmx, 2025.3-Homebrew (-: Executable: /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/bin/gmx Data prefix: /opt/homebrew/bin/../Cellar/gromacs/2025.3_1 Working dir: /Users/jiyunlee/Desktop/GROMACS Command line: gmx pdb2gmx -f complex.pdb -o complex_processed.gro -p topol.top -i posre.itp -water tip3p -ff charmm27 -ignh -merge no Using the Charmm27 force field in directory charmm27.ff going to rename charmm27.ff/aminoacids.r2b Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/aminoacids.r2b going to rename charmm27.ff/rna.r2b Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/rna.r2b Reading complex.pdb... Read '', 7442 atoms Analyzing pdb file Splitting chemical chains based on TER records or chain id changing. There are 3 chains and 0 blocks of water and 960 residues with 7442 atoms chain #res #atoms 1 'A' 313 2460 2 'Z' 1 1 3 'B' 646 4981 All occupancies are one All occupancies are one Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/atomtypes.atp Reading residue database... (Charmm27) Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/aminoacids.rtp Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/dna.rtp Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/lipids.rtp Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/rna.rtp Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/aminoacids.hdb Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/dna.hdb Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/lipids.hdb Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/rna.hdb Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/aminoacids.n.tdb Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/dna.n.tdb Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/rna.n.tdb Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/aminoacids.c.tdb Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/dna.c.tdb Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/rna.c.tdb Back Off! I just backed up topol.top to ./#topol.top.2# Processing chain 1 'A' (2460 atoms, 313 residues) Analysing hydrogen-bonding network for automated assignment of histidine protonation. 450 donors and 448 acceptors were found. There are 757 hydrogen bonds Will use HISE for residue 9 Will use HISE for residue 121 Will use HISE for residue 132 Will use HISE for residue 150 Will use HISE for residue 195 Will use HISE for residue 217 Will use HISE for residue 239 Will use HISD for residue 266 Will use HISD for residue 268 Will use HISE for residue 273 Will use HISE for residue 278 Will use HISE for residue 280 Will use HISE for residue 310 Identified residue CYS3 as a starting terminus. Identified residue ASP315 as a ending terminus. 9 out of 9 lines of specbond.dat converted successfully Special Atom Distance matrix: CYS3 HIS9 MET20 CYS38 CYS54 MET112 HIS121 SG4 NE256 SD133 SG270 SG395 SD833 NE2906 HIS9 NE256 2.285 MET20 SD133 2.620 1.379 CYS38 SG270 2.601 2.318 1.489 CYS54 SG395 2.317 1.940 1.424 0.516 MET112 SD833 2.414 3.159 2.253 1.998 2.244 HIS121 NE2906 2.394 3.364 3.376 2.267 2.056 3.197 HIS132 NE2992 3.147 4.289 3.405 2.966 3.255 1.159 3.746 CYS140 SG1041 3.224 3.921 2.880 2.645 2.979 0.861 3.911 CYS149 SG1117 2.568 4.147 3.528 2.853 3.029 1.492 2.953 HIS150 NE21127 2.920 4.423 3.782 2.807 3.013 1.944 2.626 CYS154 SG1161 1.433 3.057 2.688 2.396 2.402 1.250 2.662 CYS187 SG1408 3.156 2.055 0.968 2.215 2.293 2.280 4.205 MET188 SD1415 2.650 1.829 0.551 1.527 1.610 1.817 3.494 HIS195 NE21479 3.128 1.100 1.160 2.554 2.357 3.276 4.174 MET203 SD1538 2.273 1.379 0.378 1.355 1.269 1.967 3.117 HIS217 NE21644 2.639 3.305 2.520 2.814 2.980 1.047 4.041 MET219 SD1659 2.397 3.489 2.851 2.962 3.091 1.104 3.841 CYS226 SG1710 3.444 4.582 4.066 4.391 4.506 2.501 5.171 HIS239 NE21821 3.473 4.369 3.517 3.617 3.859 1.650 4.700 MET243 SD1860 3.236 3.630 2.512 2.470 2.807 0.894 4.003 CYS249 SG1903 2.798 2.813 1.629 1.646 1.959 0.907 3.457 HIS266 NE22044 2.064 2.739 2.039 2.287 2.389 0.825 3.461 HIS268 NE22061 2.240 2.965 2.170 2.256 2.417 0.547 3.444 HIS273 NE22110 3.599 3.804 2.558 2.200 2.640 1.282 3.880 HIS278 NE22141 2.496 2.863 2.030 2.462 2.609 1.017 3.870 HIS280 NE22163 2.867 3.180 2.305 2.791 2.969 1.261 4.255 HIS310 NE22421 2.243 3.269 3.053 3.581 3.555 2.145 4.316 HIS132 CYS140 CYS149 HIS150 CYS154 CYS187 MET188 NE2992 SG1041 SG1117 NE21127 SG1161 SG1408 SD1415 CYS140 SG1041 0.798 CYS149 SG1117 1.075 1.707 HIS150 NE21127 1.582 2.150 0.787 CYS154 SG1161 1.725 1.933 1.237 1.786 CYS187 SG1408 3.341 2.682 3.730 4.105 2.965 MET188 SD1415 2.949 2.374 3.194 3.499 2.439 0.724 HIS195 NE21479 4.421 3.881 4.541 4.858 3.548 1.407 1.559 MET203 SD1538 3.126 2.657 3.190 3.463 2.318 1.128 0.539 HIS217 NE21644 1.547 1.183 2.094 2.752 1.630 2.216 2.045 MET219 SD1659 1.343 1.316 1.683 2.413 1.254 2.696 2.425 CYS226 SG1710 2.279 2.355 2.729 3.504 2.510 3.692 3.633 HIS239 NE21821 1.295 1.180 2.147 2.816 2.233 3.135 3.007 MET243 SD1860 1.299 0.513 2.113 2.540 2.092 2.219 1.981 CYS249 SG1903 1.911 1.287 2.357 2.673 1.986 1.545 1.128 HIS266 NE22044 1.725 1.420 1.969 2.558 1.207 1.966 1.632 HIS268 NE22061 1.435 1.119 1.765 2.341 1.202 2.092 1.730 HIS273 NE22110 1.640 0.994 2.350 2.534 2.507 2.392 2.077 HIS278 NE22141 1.849 1.365 2.311 2.896 1.680 1.732 1.555 HIS280 NE22163 1.894 1.352 2.508 3.116 2.001 1.850 1.804 HIS310 NE22421 2.560 2.495 2.677 3.417 1.820 2.860 2.752 HIS195 MET203 HIS217 MET219 CYS226 HIS239 MET243 NE21479 SD1538 NE21644 SD1659 SG1710 NE21821 SD1860 MET203 SD1538 1.407 HIS217 NE21644 3.286 2.272 MET219 SD1659 3.637 2.552 0.591 CYS226 SG1710 4.639 3.807 1.654 1.447 HIS239 NE21821 4.314 3.284 1.066 1.078 1.282 MET243 SD1860 3.479 2.332 1.084 1.430 2.485 1.359 CYS249 SG1903 2.680 1.460 1.408 1.768 3.050 2.142 0.926 HIS266 NE22044 2.859 1.740 0.660 0.813 2.138 1.664 1.299 HIS268 NE22061 3.065 1.878 0.613 0.750 2.140 1.496 1.047 HIS273 NE22110 3.620 2.433 1.860 2.152 3.270 2.084 0.809 HIS278 NE22141 2.798 1.798 0.501 0.979 2.096 1.531 1.109 HIS280 NE22163 3.012 2.115 0.479 1.067 1.929 1.319 1.067 HIS310 NE22421 3.477 2.774 1.390 1.231 1.447 1.974 2.469 CYS249 HIS266 HIS268 HIS273 HIS278 HIS280 SG1903 NE22044 NE22061 NE22110 NE22141 NE22163 HIS266 NE22044 1.178 HIS268 NE22061 1.056 0.313 HIS273 NE22110 1.024 1.904 1.651 HIS278 NE22141 1.086 0.483 0.562 1.780 HIS280 NE22163 1.284 0.851 0.863 1.806 0.404 HIS310 NE22421 2.568 1.428 1.633 3.215 1.537 1.607 Start terminus CYS-3: NH3+ End terminus ASP-315: COO- Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/aminoacids.arn Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/dna.arn Opening force field file /opt/homebrew/bin/../Cellar/gromacs/2025.3_1/share/gromacs/top/charmm27.ff/rna.arn Checking for duplicate atoms.... Generating any missing hydrogen atoms and/or adding termini. Now there are 313 residues with 4881 atoms Chain time... Back Off! I just backed up topol_Protein_chain_A.itp to ./#topol_Protein_chain_A.itp.2# Making bonds... Number of bonds was 4951, now 4951 Generating angles, dihedrals and pairs... Before cleaning: 13035 pairs Before cleaning: 13220 dihedrals Making cmap torsions... There are 311 cmap torsion pairs There are 13220 dihedrals, 830 impropers, 8977 angles 12933 pairs, 4951 bonds and 0 virtual sites Total mass 34910.134 a.m.u. Total charge -5.000 e Writing topology Back Off! I just backed up posre_Protein_chain_A.itp to ./#posre_Protein_chain_A.itp.2# Processing chain 2 'Z' (1 atoms, 1 residues) Residue ZN1001 has type 'Ion', assuming it is not linked into a chain. Problem with chain definition, or missing terminal residues. This chain does not appear to contain a recognized chain molecule. If this is incorrect, you can edit residuetypes.dat to modify the behavior. 9 out of 9 lines of specbond.dat converted successfully ------------------------------------------------------- Program: gmx pdb2gmx, version 2025.3-Homebrew Source file: src/gromacs/gmxpreprocess/resall.cpp (line 625) Fatal error: Residue 'ZN' not found in residue topology database For more information and tips for troubleshooting, please check the GROMACS website at https://manual.gromacs.org/current/user-guide/run-time-errors.html ``` i opened by charmm27.ff file and i think this file does not contain any errors part of atomtypes.atp ```auto ZN 65.370000 ; zinc (II) cation ``` part of ions.itp ```auto [moleculetype] ; molname nrexcl ZN 1 [atoms] ; id at type res nr residu name at name cg nr charge 1 ZN 1 ZN ZN 1 2 ``` part of the aminoacids.rtp ```auto [ZN2] [atoms] ZN ZN 2.00 0 ``` I could not find any thing like residuetypes.dat in my charmm27.ff file