Molecule type 'Protein_chain_A' contains no atoms

Ntieche1
Fri, 30 May 2025 19:03:19 +0000
User discussions

GROMACS version:
GROMACS modification: Yes/No
Here post your question
I am a newsly user trying to perform molecular dynamics with the basic gramocs tutorials without any modifications and I have this error . I need help please : (base) ntieche@WNDPC:~/molecular_dynamics/Protein_ligand_MD$ gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
:-) GROMACS - gmx grompp, 2023.3-Ubuntu_2023.3_1ubuntu3 (-:

Executable: /usr/bin/gmx
Data prefix: /usr
Working dir: /home/ntieche/molecular_dynamics/Protein_ligand_MD
Command line:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

Ignoring obsolete mdp entry ‘title’
Ignoring obsolete mdp entry ‘ns_type’

NOTE 1 [file ions.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.

Setting the LD random seed to 231176915

Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1

Generated 117432 of the 167910 1-4 parameter combinations

Program: gmx grompp, version 2023.3-Ubuntu_2023.3_1ubuntu3
Source file: src/gromacs/gmxpreprocess/topio.cpp (line 897)

Fatal error:
Molecule type ‘Protein_chain_A’ contains no atoms

For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation

I need help please.
Thank you

2 posts - 2 participants