Error while generating the topology by gmx pdb2gmx

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1

GROMACS version:
GROMACS modification: Yes/No
Here post your question I have lipid.pdb file, while giving command gmx pdb2gmx -f lipid.pdb -o lipid.gro …following error comes out

Warning: Starting residue KS7G0 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 KS7G 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

Program: gmx pdb2gmx, version 2018.1
Source file: src/gromacs/gmxpreprocess/resall.cpp (line 639)

Fatal error:
Residue ‘KS7G’ not found in residue topology database

Please help me …I have to generate lipid.gro, topol.top and porse.itp file.

2

Hi,

As indicated in the output, your PDB contains a residue called KS7G, which is not a standard residue. If you want to keep it (e.g. it’s a ligand you want to simulate), follow established tutorials for adding residues to the force field of your choice, or find an existing parametrization in the literature. If it’s e.g. a solvent residue that is an artifact of the structure determination method, just remove it.