GROMACS version:
GROMACS modification: Yes/No
Here post your question
Dear Experts,
I install the gromacs that suppor the constant ph MD.
Then I do the following steps.
-
gmx pdb2gmx -o prot.gro -ignh -ff charmm36m-lambdadyn -water tip3p -ldglu -ldhis -ldasp -ldtyr -ldlys -f output.gro
-
gmx editconf -f prot.gro -o box.gro -box 30 30 30 -c -bt cubic
-
gmx solvate -cs spc216.gro -cp box.gro -p topol.top -o solv.gro
-
sed ‘s/HOH/SOL/g’ solv.gro > SOLV.gro
-
gmx grompp -f genion.mdp -c SOLV.gro -o genion.tpr -p topol.top -maxwarn 1
-
gmx genion -s genion.tpr -o solvions.gro -p topol.top -pname SOD -nname CLA -conc 0.15 -neutral -cphcoupled -rminprotld 2.0 -rminld 3.0 -rtolld 0.3 -nobackup
But In the step 6th I got the following error message.
umber of (3-atomic) solvent molecules: 877739
Processing topology
Replacing 4920 solute molecules in topology file (topol.top) by 2439 SOD and 2481 CLA ions, and 72 lambda dynamics counterions.
Using random seed -1082671106.
Lambda dyn counterion: Determining solvent molecules not too close to non solvent…
For the solvent search, min. dist to non-solvent: 2.00, distance to residue 2.70 - 3.30 (tolerance included)
877600 of 877739
Found 867438 suitable solvents
Lambda dyn counterion: Determining solvent molecules suitable for each residue…
The following protonable residues have 0 suitable water for counterion/buffer placement: 2 19 31 32 38 39 58
Program: gmx genion, version 2024-dev-20241209-eba91f0-unknown
Source file: src/gromacs/gmxpreprocess/genion.cpp (line 321)
Fatal error:
Some residue have no suitable solvent for buffer/counterion placement. Maybe
try a bigger box?