GROMACS version: gromacs/2021.4_cuda-11.4.3 [supercomputer]
GROMACS modification: No
Hello everyone! I am currently trying to the prepare protein-ligand complex. As I tried to do the grompp command, I’ve encountered 24 errors. [See below] I am using the latest CHARMM folder (jul2021) and have used the CGenFF in generating the .str file. I’d be happy if anyone could help. Thanks!
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GROMACS: gmx grompp, version 2021.4
Executable: /opt/hpcc/GPU_P40/gromacs/2021.4_cuda-11.4.3/bin/gmx
Data prefix: /opt/hpcc/GPU_P40/gromacs/2021.4_cuda-11.4.3
Working dir: /scratch1/kaye.conejos/trial1/mdd
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 -22025737
Generated 167799 of the 167910 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 117519 of the 167910 1-4 parameter combinations
ERROR 1 [file unl.itp, line 169]:
No default U-B types
ERROR 2 [file unl.itp, line 170]:
No default U-B types
ERROR 3 [file unl.itp, line 174]:
No default U-B types
ERROR 4 [file unl.itp, line 186]:
No default U-B types
ERROR 5 [file unl.itp, line 228]:
No default U-B types
ERROR 6 [file unl.itp, line 230]:
No default U-B types
ERROR 7 [file unl.itp, line 234]:
No default Proper Dih. types
ERROR 8 [file unl.itp, line 235]:
No default Proper Dih. types
ERROR 9 [file unl.itp, line 236]:
No default Proper Dih. types
ERROR 10 [file unl.itp, line 237]:
No default Proper Dih. types
ERROR 11 [file unl.itp, line 238]:
No default Proper Dih. types
ERROR 12 [file unl.itp, line 239]:
No default Proper Dih. types
ERROR 13 [file unl.itp, line 240]:
No default Proper Dih. types
ERROR 14 [file unl.itp, line 242]:
No default Proper Dih. types
ERROR 15 [file unl.itp, line 244]:
No default Proper Dih. types
ERROR 16 [file unl.itp, line 245]:
No default Proper Dih. types
ERROR 17 [file unl.itp, line 246]:
No default Proper Dih. types
ERROR 18 [file unl.itp, line 247]:
No default Proper Dih. types
ERROR 19 [file unl.itp, line 254]:
No default Proper Dih. types
ERROR 20 [file unl.itp, line 258]:
No default Proper Dih. types
ERROR 21 [file unl.itp, line 260]:
No default Proper Dih. types
ERROR 22 [file unl.itp, line 270]:
No default Proper Dih. types
ERROR 23 [file unl.itp, line 271]:
No default Proper Dih. types
ERROR 24 [file unl.itp, line 272]:
No default Proper Dih. types
Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_B’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_C’
Excluding 3 bonded neighbours molecule type ‘Protein_chain_D’
Excluding 3 bonded neighbours molecule type ‘UNL’
Excluding 2 bonded neighbours molecule type ‘SOL’
NOTE 2 [file topol.top, line 59]:
System has non-zero total charge: -4.000000
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 2021.4
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1963)
Fatal error:
There were 24 errors in input file(s)