GROMACS version: version 2020.1-Ubuntu-2020.1-1
GROMACS modification: Yes/No
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Hello,
I am a very new user and have been successful to running other simulations. This is my largest, I have attempted (60-mer icosahedral). I got this error and I am a bit unsure as to how I can fix it or by pass maybe?? I copied and pasted below. Please help me and be gentle because I am new to the field.
GROMACS: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Executable: /usr/bin/gmx
Data prefix: /usr
Working dir:
Command line:
gmx grompp -f em.mdp -p topol.top -c solvate.gro -o em.tpr
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 -1437330375
Generated 165 of the 1596 non-bonded parameter combinations
ERROR 1 [file topol_Protein_chain_a.itp, line 22]:
moleculetype Protein_chain_a is redefined
There was 1 note
Program: gmx grompp, version 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/toppush.cpp (line 1474)
Fatal error:
There was 1 error in input file(s)
Thank you,
Heather Noriega