Residue 1 named SYR of a molecule in the input file was mapped to an entry in the topology database

User discussions
1

GROMACS version: 2021.4
GROMACS modification: Yes/No
Hello,

I am trying to create a topology file for GROMACS of a simulation cell of lignin, but this error occur:

Fatal error:
Residue 1 named SYR of a molecule in the input file was mapped
to an entry in the topology database, but the atom O8 used in
that entry is not found in the input file. Perhaps your atom
and/or residue naming needs to be fixed.

I have tried using Swiss pdb for fixing the structure, but I keep getting an error no matter what. I am not even sure how to fix the atom naming. Can someone please help me with how I can fix this?

2

This is the output from pdb2gmx :
(base) silvio@Gomez:~/Documents/intento1/molecular_dynamics/sistema$ gmx1 pdb2gmx -f molecule.pdb -o molecule.gro
:-) GROMACS - gmx pdb2gmx, 2021.4 (-:

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GROMACS: gmx pdb2gmx, version 2021.4
Executable: /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/build/bin/gmx1
Data prefix: /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4 (source tree)
Working dir: /home/silvio/Documents/intento1/molecular_dynamics/sistema
Command line:
gmx1 pdb2gmx -f molecule.pdb -o molecule.gro

Select the Force Field:

From ‘/home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/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: CHARMM FF

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)
8

Using the Charmm36 force field in directory charmm36.ff
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.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
8

going to rename charmm36.ff/aminoacids.r2b
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/aminoacids.r2b

going to rename charmm36.ff/carb.r2b
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/carb.r2b

going to rename charmm36.ff/cgenff.r2b
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/cgenff.r2b

going to rename charmm36.ff/ethers.r2b
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/ethers.r2b

going to rename charmm36.ff/lignin.r2b
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/lignin.r2b

going to rename charmm36.ff/lipid.r2b
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/lipid.r2b

going to rename charmm36.ff/metals.r2b
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/metals.r2b

going to rename charmm36.ff/na.r2b
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/na.r2b

going to rename charmm36.ff/silicates.r2b
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/silicates.r2b

going to rename charmm36.ff/solvent.r2b
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/solvent.r2b
Reading molecule.pdb…
Read ‘’, 172 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 6 residues with 172 atoms

chain #res #atoms

1 ‘L’ 6 172

All occupancies are one
All occupancies are one
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/atomtypes.atp

Reading residue database… (Charmm36)
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/aminoacids.rtp
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/carb.rtp
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/cgenff.rtp
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/ethers.rtp
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/lignin.rtp
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/lipid.rtp
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/metals.rtp
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/na.rtp
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/silicates.rtp
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/solvent.rtp
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/lignin.hdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/aminoacids.n.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/carb.n.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/cgenff.n.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/ethers.n.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/lignin.n.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/lipid.n.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/metals.n.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/na.n.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/silicates.n.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/solvent.n.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/aminoacids.c.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/carb.c.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/cgenff.c.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/ethers.c.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/lignin.c.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/lipid.c.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/metals.c.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/na.c.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/silicates.c.tdb
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/solvent.c.tdb

Processing chain 1 ‘L’ (172 atoms, 6 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
Opening force field file /home/silvio/Documents/software/gromacs/gromacs-2021.4/gromacs-2021.4/share/top/charmm36.ff/aminoacids.arn

Checking for duplicate atoms…

Generating any missing hydrogen atoms and/or adding termini.

Program: gmx pdb2gmx, version 2021.4
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 151)

Fatal error:
Residue 1 named SYR of a molecule in the input file was mapped
to an entry in the topology database, but the atom O8 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

3

Whatever SYR is requires an atom named O8 in its topology, but that atom is not found in your input coordinate file. Rename the atoms in the PDB file to correspond to those required by the residue definition in the .rtp entry.

4

Thanks for your reply
I dont know how to rename the atoms in my PDB, because the lignin molecules are united by BO4 linkage, so the atom O8 correspond to atom O4 of that linkage.

5

Then you need to rename anything called O8 as O4.