GROMACS version:2023.1
GROMACS modification: Yes/No
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I am using gromacs to run a simulation for glibenclamide as a ligand and ATP-sensitive potassium channel protein, however i am keep getting the error due to No default Improper Dih. types
how I can solve the issue?
below is the command the output message
gmx grompp -f ions.mdp -c box_sol.gro -p topol.top -o ION.tpr
:-) GROMACS - gmx grompp, 2023.1 (-:
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/muhanad/MD/glibenclamide-ATP sensitive potassium channel
Command line:
gmx grompp -f ions.mdp -c box_sol.gro -p topol.top -o ION.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 -680659265
Generated 174825 of the 174936 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 124435 of the 174936 1-4 parameter combinations
ERROR 1 [file topol.top, line 169366]:
No default Improper Dih. types
ERROR 2 [file topol.top, line 170184]:
No default Improper Dih. types
Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘LIG’
Excluding 2 bonded neighbours molecule type ‘SOL’
NOTE 2 [file topol.top, line 171983]:
System has non-zero total charge: 25.000000 Total charge should normally be an integer. See Floating point arithmetic — GROMACS webpage https://www.gromacs.org documentation for discussion on how close it should be to an integer.
There were 2 NOTEs
Program: gmx grompp, version 2023.1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2198)
Fatal error:
There were 2 errors in input file(s)
For more information and tips for troubleshooting, please check the GROMACS
website at Common Errors — GROMACS webpage https://www.gromacs.org documentation