GROMACS version: 2022.4
GROMACS modification: No
Hi,
I’m facing a weird problem with a pdb file. I have pdb file with two chains and it’s giving some error which I can’t understand at the pdb2gmx stage.
I have modeled this crystal structure and removed all ligands and ions and trying to generate the .gro file.
However, as per the error I checked the pdb:
- there’s no LEU at 140 residue position, it’s ALA ! (PDB starts at residue 6. Res 146 is also not LEU). I’m not sure where I’m making a mistake here.
- I checked all LEU residues, everyone has CA as per PDB naming convention and there’s no chain break in the PDB (except two normal chains).
gmx pdb2gmx -f model.pdb -o onlyprotein_processed.gro -ter -ignh
:-) GROMACS - gmx pdb2gmx, 2022.4 (-:
Executable: /programs/x86_64-linux/gromacs/2022.4_cu11.5.2/bin/…/…/gromacs-2022.4-dzjw/bin/gmx
Data prefix: /programs/x86_64-linux/gromacs/2022.4_cu11.5.2/bin/…/…/gromacs-2022.4-dzjw
Working dir: /home/testMD
Command line:
gmx pdb2gmx -f model.pdb -o processed.gro -ter -ignh
Select the Force Field:
From ‘/programs/x86_64-linux/gromacs/2022.4_cu11.5.2/bin/…/…/gromacs-2022.4-dzjw/share/gromacs/top’:
1: AMBER03 protein, nucleic AMBER94 (Duan et al., J. Comp. Chem. 24, 1999-2012, 2003)
2: AMBER94 force field (Cornell et al., JACS 117, 5179-5197, 1995)
3: AMBER96 protein, nucleic AMBER94 (Kollman et al., Acc. Chem. Res. 29, 461-469, 1996)
4: AMBER99 protein, nucleic AMBER94 (Wang et al., J. Comp. Chem. 21, 1049-1074, 2000)
5: AMBER99SB protein, nucleic AMBER94 (Hornak et al., Proteins 65, 712-725, 2006)
6: AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
7: AMBERGS force field (Garcia & Sanbonmatsu, PNAS 99, 2782-2787, 2002)
8: CHARMM27 all-atom force field (CHARM22 plus CMAP for proteins)
9: GROMOS96 43a1 force field
10: GROMOS96 43a2 force field (improved alkane dihedrals)
11: GROMOS96 45a3 force field (Schuler JCC 2001 22 1205)
12: GROMOS96 53a5 force field (JCC 2004 vol 25 pag 1656)
13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
14: GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9)
15: OPLS-AA/L all-atom force field (2001 aminoacid dihedrals)
13
Using the Gromos53a6 force field in directory gromos53a6.ff
Opening force field file /programs/x86_64-linux/gromacs/2022.4_cu11.5.2/bin/…/…/gromacs-2022.4-dzjw/share/gromacs/top/gromos53a6.ff/watermodels.dat
Select the Water Model:
1: SPC simple point charge, recommended
2: SPC/E extended simple point charge
3: None
1
going to rename gromos53a6.ff/aminoacids.r2b
Opening force field file /programs/x86_64-linux/gromacs/2022.4_cu11.5.2/bin/…/…/gromacs-2022.4-dzjw/share/gromacs/top/gromos53a6.ff/aminoacids.r2b
Reading model.pdb…
Read ‘’, 4067 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 2 chains and 0 blocks of water and 528 residues with 4067 atoms
chain #res #atoms
1 ‘A’ 264 2033
2 ‘B’ 264 2034
there were 0 atoms with zero occupancy and 72 atoms with occupancy unequal to one (out of 4067 atoms). Check your pdb file.
there were 0 atoms with zero occupancy and 72 atoms with occupancy unequal to one (out of 4067 atoms). Check your pdb file.
Opening force field file /programs/x86_64-linux/gromacs/2022.4_cu11.5.2/bin/…/…/gromacs-2022.4-dzjw/share/gromacs/top/gromos53a6.ff/atomtypes.atp
Reading residue database… (Gromos53a6)
Opening force field file /programs/x86_64-linux/gromacs/2022.4_cu11.5.2/bin/…/…/gromacs-2022.4-dzjw/share/gromacs/top/gromos53a6.ff/aminoacids.rtp
Using default: not generating all possible dihedrals
Using default: excluding 3 bonded neighbors
Using default: generating 1,4 H–H interactions
Using default: removing proper dihedrals found on the same bond as a proper dihedral
Using default: removing proper dihedrals found on the same bond as a proper dihedral
Opening force field file /programs/x86_64-linux/gromacs/2022.4_cu11.5.2/bin/…/…/gromacs-2022.4-dzjw/share/gromacs/top/gromos53a6.ff/aminoacids.hdb
Opening force field file /programs/x86_64-linux/gromacs/2022.4_cu11.5.2/bin/…/…/gromacs-2022.4-dzjw/share/gromacs/top/gromos53a6.ff/aminoacids.n.tdb
Opening force field file /programs/x86_64-linux/gromacs/2022.4_cu11.5.2/bin/…/…/gromacs-2022.4-dzjw/share/gromacs/top/gromos53a6.ff/aminoacids.c.tdb
Back Off! I just backed up topol.top to ./#topol.top.5#
Processing chain 1 ‘A’ (2033 atoms, 264 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 377 donors and 351 acceptors were found.
There are 512 hydrogen bonds
Will use HISE for residue 32
Will use HISE for residue 151
Will use HISE for residue 172
Will use HISE for residue 194
Will use HISE for residue 258
Will use HISE for residue 263
Identified residue LEU6 as a starting terminus.
Identified residue ILE269 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
HIS32 CYS53 MET135 HIS151 MET159 CYS170 HIS172
NE2191 SG361 SD946 NE21068 SD1131 SG1228 NE21252
CYS53 SG361 3.308
MET135 SD946 3.172 5.762
HIS151 NE21068 5.232 7.646 2.637
MET159 SD1131 6.242 7.908 3.565 2.267
CYS170 SG1228 5.500 7.187 2.775 2.357 1.040
HIS172 NE21252 5.070 7.076 2.389 1.295 1.320 1.136
CYS184 SG1333 3.888 5.723 2.017 2.103 2.476 2.048 1.434
HIS194 NE21412 3.840 4.770 3.615 3.747 4.009 3.793 3.287
CYS208 SG1535 3.371 4.857 2.282 2.990 3.182 2.657 2.291
MET249 SD1871 3.756 5.644 1.571 2.283 2.494 1.809 1.460
HIS258 NE21950 5.157 7.399 2.084 1.587 1.817 1.311 1.058
HIS263 NE21989 5.034 7.283 1.901 2.074 2.200 1.491 1.521
CYS184 HIS194 CYS208 MET249 HIS258
SG1333 NE21412 SG1535 SD1871 NE21950
HIS194 NE21412 2.004
CYS208 SG1535 0.906 1.488
MET249 SD1871 0.658 2.478 1.083
HIS258 NE21950 2.135 4.128 2.908 1.858
HIS263 NE21989 2.368 4.365 3.033 1.950 0.551
Select start terminus type for LEU-6
0: NH3+
1: NH2
2: None
0
Start terminus LEU-6: NH3+
Select end terminus type for ILE-269
0: COO-
1: COOH
2: None
0
End terminus ILE-269: COO-
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
Checking for duplicate atoms…
Now there are 2009 atoms. Deleted 24 duplicates.
Generating any missing hydrogen atoms and/or adding termini.
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
WARNING: Duplicate line found in or between hackblock and rtp entries
Program: gmx pdb2gmx, version 2022.4
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 154)
Fatal error:
Residue 140 named LEU of a molecule in the input file was mapped
to an entry in the topology database, but the atom CA used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation
Please suggest.
Thanks