Residue 42 named TYR of a molecule in the input file was mapped to an entry in the topology database

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1

GROMACS version:2023
GROMACS modification: Yes
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kayode@kayode:~/Documents/Carrot/scolimoside$ gmx pdb2gmx -f REC.pdb -ignh
:-) GROMACS - gmx pdb2gmx, 2023 (-:

Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/kayode/Documents/Carrot/scolimoside
Command line:
gmx pdb2gmx -f REC.pdb -ignh

Select the Force Field:

From ‘/usr/local/gromacs/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)
8

Using the Charmm27 force field in directory charmm27.ff
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/watermodels.dat

Select the Water Model:

1: TIP3P TIP 3-point, recommended

2: TIP4P TIP 4-point

3: TIPS3P CHARMM TIP 3-point with LJ on H’s

4: TIP5P TIP 5-point (see OPLS/AA not compatible with TIP5P - Redmine #1348 (#1348) · Issues · GROMACS / GROMACS · GitLab for issues)

5: SPC simple point charge

6: SPC/E extended simple point charge

7: None
1

going to rename charmm27.ff/aminoacids.r2b
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.r2b

going to rename charmm27.ff/rna.r2b
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.r2b
Reading REC.pdb…
WARNING: all CONECT records are ignored
Read ‘’, 2308 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 286 residues with 2308 atoms

chain #res #atoms

1 ‘P’ 286 2308

All occupancies are one
All occupancies are one
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/atomtypes.atp

Reading residue database… (Charmm27)
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.rtp
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.rtp
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.rtp
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.rtp
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/lipids.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.hdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.n.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.n.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.n.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.c.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.c.tdb
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.c.tdb

Back Off! I just backed up topol.top to ./#topol.top.5#

Processing chain 1 ‘P’ (2308 atoms, 286 residues)

Identified residue GLN66 as a starting terminus.

Identified residue THR359 as a ending terminus.
8 out of 8 lines of specbond.dat converted successfully
Special Atom Distance matrix:
MET134 CYS181 MET217 CYS260 CYS270 CYS327
SD549 SG940 SD1214 SG1529 SG1603 SG2061
CYS181 SG940 2.705
MET217 SD1214 2.044 1.012
CYS260 SG1529 2.213 3.043 3.120
CYS270 SG1603 2.322 2.083 2.317 1.427
CYS327 SG2061 2.623 2.857 3.140 0.770 1.582
MET330 SD2086 3.101 2.954 3.387 1.264 1.827 0.528
Start terminus GLN-66: NH3+
End terminus THR-359: COO-
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/aminoacids.arn
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/dna.arn
Opening force field file /usr/local/gromacs/share/gromacs/top/charmm27.ff/rna.arn

Checking for duplicate atoms…

Now there are 2292 atoms. Deleted 16 duplicates.

Generating any missing hydrogen atoms and/or adding termini.

Program: gmx pdb2gmx, version 2023
Source file: src/gromacs/gmxpreprocess/pgutil.cpp (line 154)

Fatal error:
Residue 42 named TYR of a molecule in the input file was mapped
to an entry in the topology database, but the atom C 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

kayode@kayode:~/Documents/Carrot/scolimoside$

2

It seems one of the tyrosine residues in your pdb file is missing a carbon atom, you may need to look into your pdb file with a text editor to check whether something was mislabeled, and if there is actually a carbon atom missing, then you’ll need to get a new pdb file with all the correct atoms for each residue.

If the change to the residue was purposeful, then you need to define a topology file for the altered residue, which can be done using a number of servers (Protein-Ligand Complex, for CHARMM, you would be using CGenFF) and include that data in your topology file (if you’re defining your own topology, you may need to make your topol.top file from scratch rather than generate it with pdb2gmx)