I’m not sure how to resolve this issue. I generated the .str file using the online CGenFF platform (which I assume is up to date), but I’m having trouble figuring out how to fix the error.
ERROR 1 [file dd.itp, line 198]:
No default Proper Dih. types
ERROR 2 [file dd.itp, line 200]:
No default Proper Dih. types
ERROR 3 [file dd.itp, line 224]:
No default Proper Dih. types
ERROR 4 [file dd.itp, line 226]:
No default Proper Dih. types
Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’
Excluding 3 bonded neighbours molecule type ‘Other_chain_A2’
Excluding 3 bonded neighbours molecule type ‘dd’
Excluding 2 bonded neighbours molecule type ‘SOL’
NOTE 2 [file topol.top, line 55]:
System has non-zero total charge: -1.000000
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 2020.1-Ubuntu-2020.1-1
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 1928)
Fatal error:
There were 4 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
(base) hindol@hindol_cha:/mnt/c/Users/hindo/Desktop/Academics/Internships/St. Xavier’s (Autonomous) college/Computational biology/MD Simulation/B. subtilis/1svi_dd (Dimethyl diethylmalonate)$