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Hi, I am currently new to GROMACS and having problem to prepare protein topology. The errors are shown as below:
Residue 3 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
Here also I attach the output of my terminal:
gmx pdb2gmx -f 1aj6_clean.pdb -o 1aj6_processed.gro
:-) GROMACS - gmx pdb2gmx, 2020.1-Ubuntu-2020.1-1 (-:
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GROMACS: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/user/Desktop/khadijah/new
Command line:
gmx pdb2gmx -f 1aj6_clean.pdb -o 1aj6_processed.gro
Select the Force Field:
From current directory:
1: CHARMM all-atom force field
From ‘/usr/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 1aj6_clean.pdb…
WARNING: all CONECT records are ignored
Read ‘GYRASE’, 1459 atoms
Analyzing pdb file
Splitting chemical chains based on TER records or chain id changing.
There are 1 chains and 0 blocks of water and 194 residues with 1459 atoms
chain #res #atoms
1 ‘A’ 194 1459
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
Processing chain 1 ‘A’ (1459 atoms, 194 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 286 donors and 274 acceptors were found.
There are 407 hydrogen bonds
Will use HISE for residue 37
Will use HISD for residue 38
Will use HISE for residue 55
Will use HISE for residue 64
Will use HISE for residue 99
Will use HISE for residue 116
Will use HISH for residue 136
Will use HISE for residue 141
Will use HISE for residue 147
Will use HISE for residue 215
Will use HISE for residue 217
Identified residue VAL12 as a starting terminus.
Identified residue HIS217 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET25 HIS37 HIS38 MET39 HIS55 CYS56 HIS64
SD101 NE2190 NE2200 SD207 NE2324 SG330 NE2393
HIS37 NE2190 2.018
HIS38 NE2200 1.326 1.259
MET39 SD207 1.476 1.126 0.796
HIS55 NE2324 3.456 3.146 2.360 2.644
CYS56 SG330 3.165 2.312 1.883 2.083 1.030
HIS64 NE2393 3.068 1.589 2.029 1.606 2.610 1.730
MET95 SD572 2.300 2.109 1.498 1.176 1.897 1.631 1.611
HIS99 NE2605 1.447 2.633 1.471 1.662 2.460 2.565 2.989
HIS116 NE2666 1.745 1.869 0.766 1.515 1.966 1.709 2.473
HIS136 NE2808 3.530 3.148 2.568 2.437 1.328 1.504 2.139
HIS141 NE2848 3.723 3.284 2.814 2.564 1.762 1.832 2.131
HIS147 NE2907 1.991 1.907 1.910 1.144 3.419 2.934 1.956
MET166 SD1029 2.959 1.917 1.891 1.526 2.048 1.346 0.704
HIS215 NE21438 3.683 2.246 2.369 2.564 2.073 1.151 1.789
HIS217 NE21459 3.910 2.410 2.628 2.890 2.457 1.599 2.176
MET95 HIS99 HIS116 HIS136 HIS141 HIS147 MET166
SD572 NE2605 NE2666 NE2808 NE2848 NE2907 SD1029
HIS99 NE2605 1.595
HIS116 NE2666 1.801 1.503
HIS136 NE2808 1.325 2.511 2.554
HIS141 NE2848 1.442 2.751 2.893 0.441
HIS147 NE2907 1.557 2.178 2.603 2.776 2.729
MET166 SD1029 1.051 2.561 2.223 1.450 1.469 1.915
HIS215 NE21438 2.514 3.467 2.290 2.515 2.746 3.441 1.847
HIS217 NE21459 2.967 3.809 2.513 3.009 3.248 3.808 2.317
HIS215
NE21438
HIS217 NE21459 0.505
Start terminus VAL-12: NH3+
End terminus HIS-217: COO-
Opening force field file ./charmm36-jul2022.ff/aminoacids.arn
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Program: gmx pdb2gmx, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 130)
Fatal error:
Residue 3 named LYS of a molecule in the input file was mapped
to an entry in the topology database, but the atom CG used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.
I hope that anyone can help me with this error. Thank you.