GROMACS version:gromacs/2021.4-cuda-11.6.0
GROMACS modification: Yes/No
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When I was trying to add ions to my system, I used the following command:
gmx_mpi grompp -f ions.mdp -c 1ane_solv.gro -r 1ane_solv.gro -p topol.top -o ions.tpr -maxwarn 4
But I get the errors like this:
ERROR 1 [file topol.top, line 11245]:
No default Proper Dih. types
ERROR 2 [file topol.top, line 11485]:
No default Proper Dih. types
ERROR 3 [file topol.top, line 12002]:
No default Proper Dih. types
ERROR 4 [file topol.top, line 12003]:
No default Proper Dih. types
ERROR 5 [file topol.top, line 12050]:
No default Proper Dih. types
ERROR 6 [file topol.top, line 12051]:
No default Proper Dih. types
ERROR 7 [file topol.top, line 12198]:
No default Proper Dih. types
ERROR 8 [file topol.top, line 12277]:
No default Proper Dih. types
ERROR 9 [file topol.top, line 12380]:
No default Proper Dih. types
ERROR 10 [file topol.top, line 12454]:
No default Proper Dih. types
ERROR 11 [file topol.top, line 12455]:
No default Proper Dih. types
ERROR 12 [file topol.top, line 12521]:
No default Proper Dih. types
ERROR 13 [file topol.top, line 12615]:
No default Proper Dih. types
ERROR 14 [file topol.top, line 12709]:
No default Proper Dih. types
I used GROMOS96 54a7 force field (Eur. Biophys. J. (2011), 40, 843-856, DOI: 10.1007/s00249-011-0700-9),
And the following are steps before add ions,
#Make the position restraint files.
echo “Make the position restraint files.” >&2
${GMXRUN} pdb2gmx -f $1.pdb -o 1_processed.gro -water spce -posrefc 250 -i posre250.itp < pdbgmx.txt
{GMXRUN} pdb2gmx -f $1.pdb -o 1_processed.gro -water spce -posrefc 500 -i posre500.itp < pdbgmx.txt
{GMXRUN} pdb2gmx -f $1.pdb -o 1_processed.gro -water spce -posrefc 750 -i posre750.itp < pdbgmx.txt
{GMXRUN} pdb2gmx -f $1.pdb -o $1_processed.gro -water spce -posrefc 1000 -i posre1000.itp < pdbgmx.txt
#Set the water box configuration
echo “Set the water box configuration” >&2
${GMXRUN} editconf -f $1_processed.gro -o $1_newbox.gro -c -d 1.0 -bt cubic
#Solvate that box
echo “Solvate that box” >&2
${GMXRUN} solvate -cp $1_newbox.gro -cs spc216.gro -o $1_solv.gro -p topol.top