ERROR (Warning: Short Bond)

GROMACS version: 2018.1
GROMACS modification: No

I’m trying to generate topology file (through pdb2gmx) for an ethane molecule, but I keep recieving the error message Warning: Short Bond (1-5 = 0 nm) between both carbons of the chain. I have created an .itp file whithin the oplsaa folder so I could make this run.

Command line:
gmx pdb2gmx -f metano.pdb -ff oplsaa -water none -o processed.gro

Using the Oplsaa force field in directory oplsaa.ff

Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.r2b
Reading metano.pdb…
Read ‘METHANE’, 8 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 1 residues with 8 atoms

chain #res #atoms
1 ’ ’ 1 8

All occupancies are one
Opening force field file /usr/share/gromacs/top/oplsaa.ff/atomtypes.atp
Atomtype 814
Reading residue database… (oplsaa)
Opening force field file /usr/share/gromacs/top/oplsaa.ff/aminoacids.rtp
Residue 53
Sorting it all out…
Opening force field file /usr/share/gromacs/top/oplsaa.ff/bcarotene.rtp
Residue 55
Sorting it all out…
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

Back Off! I just backed up topol.top to ./#topol.top.24#
Processing chain 1 (8 atoms, 1 residues)

Warning: Starting residue CH41 in chain not identified as Protein/RNA/DNA.
This chain lacks identifiers, which makes it impossible to do strict
classification of the start/end residues. Here we need to guess this residue
should not be part of the chain and instead introduce a break, but that will
be catastrophic if they should in fact be linked. Please check your structure,
and add CH4 to residuetypes.dat if this was not correct.

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

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…
Generating any missing hydrogen atoms and/or adding termini.
Now there are 1 residues with 8 atoms
Making bonds…
Warning: Short Bond (1-5 = 0 nm)
Warning: Short Bond (5-1 = 0 nm)
Number of bonds was 8, now 7
Generating angles, dihedrals and pairs…
Before cleaning: 9 pairs
Before cleaning: 9 dihedrals
Keeping all generated dihedrals
Making cmap torsions…
There are 9 dihedrals, 0 impropers, 12 angles
9 pairs, 7 bonds and 0 virtual sites
Total mass 30.070 a.m.u.
Total charge -2.280 e
Writing topology

Back Off! I just backed up posre.itp to ./#posre.itp.20#

Writing coordinate file…

Back Off! I just backed up processed.gro to ./#processed.gro.20#
--------- PLEASE NOTE ------------
You have successfully generated a topology from: metano.pdb.
The Oplsaa force field is used.
--------- ETON ESAELP ------------

GROMACS reminds you: “With four parameters I can fit an elephant, and with five I can make him wiggle his trunk.” (John von Neumann)

The bond length of zero means the coordinates of the bonded atoms are identical, therefore the structure is not physically realistic.

Also note that the fractional total charge means your residue definition is also unphysical.