These are the following error;
Command line:
gmx grompp -f em.mdp -c solv_ions.gro -p topol.top -o em.tpr
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'ns_type'
NOTE 1 [file em.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 -1925974956
Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 117519 of the 167910 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'JZ4'
Excluding 2 bonded neighbours molecule type 'SOL'
ERROR 1 [file topol.top, line 24679]:
No such moleculetype CL
There was 1 note
-------------------------------------------------------
Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 2511)
Fatal error:
There was 1 error in input file(s)
Dear Rishikesh Pandey
The grompp command tells you that
ERROR 1 [file topol.top, line 24679]:
No such moleculetype CL
which means that you probably added ions to neutralize charges but you did not add those ions (CL ions in this case) to the topology file.
Best,
Nicola
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