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
Fatal error:
Residue 'ZN' not found in residue topology database
this is the part of pdb that contains zinc ion
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
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
ZN 65.370000 ; zinc (II) cation
part of ions.itp
[ 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
[ ZN2 ]
[ atoms ]
ZN ZN 2.00 0
I could not find any thing like residuetypes.dat in my charmm27.ff file