GROMACS version: 2020.2
GROMACS modification: No
Hello, I am trying to follow the Protein-Ligand Complex tutorial but I end up in a problem
and I don’t understand what I am doing wrong.
I launch the command:
gmx editconf -f complex.gro -o newbox.gro -bt dodecahedron -d 1.0
That gives some output and a warning:
WARNING: Bad box in file complex.gro
Generated a cubic box 4.069 x 4.192 x 5.073
Read 2614 atoms
…
Then i use:
gmx solvate -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
Generating solvent configuration
Will generate new solvent configuration of 5x5x3 boxes
Solvent box contains 37314 atoms in 12438 residues
Removed 3990 solvent atoms due to solvent-solvent overlap
Removed 2430 solvent atoms due to solute-solvent overlap
Sorting configuration
Found 1 molecule type:
SOL ( 3 atoms): 10298 residues
Generated solvent containing 30894 atoms in 10298 residues
Writing generated configuration to solv.gro
Back Off! I just backed up solv.gro to ./#solv.gro.2#
Output configuration contains 33508 atoms in 10461 residues
Volume : 341.949 (nm^3)
Density : 997.119 (g/l)
Number of solvent molecules: 10298
Processing topology
Adding line for 10298 solvent molecules with resname (SOL) to topology file (topol.top)
Back Off! I just backed up topol.top to ./#topol.top.7#
And, at last:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
But here I get a fatal error:
Fatal error:
number of coordinates in coordinate file (solv.gro, 33508)
does not match topology (topol.top, 33530)
So, somewhere I am doing a mistake. But I did add the JZ4 in the topol.top under the [ molecules ].
I also added the coordinates of JZ4 in complex.gro (that originally is a copy of 3HTB_processed.gro) as described.
Any help please?