GROMACS version:
GROMACS modification: Yes/NO
Hello,
I am trying to create a topology file for GROMACS but I keep running into this error.
The PDB file I downloaded had some amino acid deletions, and the missing amino acids were repaired by the software chimera. However, when generating the top file, the error is always reported as follows:
"Using the Oplsaa force field in directory oplsaa.ff
going to rename oplsaa.ff/aminoacids.r2b
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b
Reading 2c2a_processed.pdb…
WARNING: all CONECT records are ignored
Read ‘’, 2037 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 252 residues with 2037 atoms
chain #res #atoms
1 ‘A’ 250 2005
2 ‘A’ 2 32
there were 0 atoms with zero occupancy and 37 atoms with occupancy unequal to one (out of 2037 atoms). Check your pdb file.
there were 0 atoms with zero occupancy and 37 atoms with occupancy unequal to one (out of 2037 atoms). Check your pdb file.
Opening force field file /usr/share/gromacs/top/oplsaa.ff/atomtypes.atp
Reading residue database… (Oplsaa)
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.hdb
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.n.tdb
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.c.tdb
Processing chain 1 ‘A’ (2005 atoms, 250 residues)
Analysing hydrogen-bonding network for automated assignment of histidine
protonation. 374 donors and 386 acceptors were found.
There are 538 hydrogen bonds
Will use HISE for residue 29
Will use HISE for residue 70
Will use HISE for residue 116
Will use HISE for residue 188
Will use HISD for residue 225
Identified residue MET1 as a starting terminus.
Identified residue ALA250 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET1 MET19 HIS29 HIS70 CYS99 HIS116 CYS128
SD5 SD160 NE2240 NE2567 SG813 NE2938 SG1032
MET19 SD160 2.951
HIS29 NE2240 4.305 1.779
HIS70 NE2567 5.126 2.276 1.380
CYS99 SG813 5.838 3.757 4.402 3.370
HIS116 NE2938 4.963 2.235 2.703 2.081 2.822
CYS128 SG1032 6.002 3.913 4.554 3.500 0.206 2.881
HIS188 NE21500 2.909 1.498 3.200 3.363 3.566 2.282 3.682
HIS225 NE21796 4.652 2.768 3.429 2.725 1.621 2.898 1.827
HIS188
NE21500
HIS225 NE21796 3.005
Linking CYS-99 SG-813 and CYS-128 SG-1032…
Start terminus MET-1: NH3+
End terminus ALA-250: COO-
Checking for duplicate atoms…
Generating any missing hydrogen atoms and/or adding termini.
Now there are 250 residues with 4034 atoms
Chain time…
Making bonds…
Number of bonds was 4067, now 4067
Generating angles, dihedrals and pairs…
Before cleaning: 10742 pairs
Before cleaning: 10817 dihedrals
Keeping all generated dihedrals
Making cmap torsions…
There are 10817 dihedrals, 765 impropers, 7389 angles
10688 pairs, 4067 bonds and 0 virtual sites
Total mass 28431.523 a.m.u.
Total charge -10.000 e
Writing topology
Processing chain 2 ‘A’ (32 atoms, 2 residues)
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.
8 out of 8 lines of specbond.dat converted successfully
Program: gmx pdb2gmx, version 2021.4-Ubuntu-2021.4-2
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 597)
Fatal error:
Residue ‘ADP’ not found in residue topology database
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation"
Is anyone willing to give advice? Thank you