I’m trying a MD simulation between a protein and a ligand. I opteined .itp and .gro files of ligand from prodrg server and I added it in .gro and .top file of the protein. I used the CHARMM27 force field. First error, in the cubic box: WARNING: Bad box in file 1.gro. I went ahead. gmx grompp -f ions.mdp -c water_box.gro -p 1.top -o ions.tpr → ERROR 1 [file DRGGMX.itp, line 23]: Atomtype CR1 not found.
I tried with another .itp file, generated from LigParGen, the error was: ERROR: Fatal error: Syntax error - File Ligand.itp, line 3 Last line read: ‘[ atomtypes ]’ Invalid order for directive atomtypes. How can I bypass this problem?
I’ve changed the protocol. I’ve used OPLS force field and LigParGen ligand.gro and ligand.itp but the problems still the same: WARNING: Bad box in file 1.gro (but i could continue) and Fatal error: Syntax error - File ligand.itp, line 6 Last line read: ‘[ atomtypes ]’ Invalid order for directive atomtypes, which keeps it from going.
Marco De Gennaro
Hello
you applied CHARM27 force field so you prepare you ligand topology through swissPARAM and generated zip file extract in you path folder where you keep protein for simulation.
Dear Marco De Gennaro
The bad box outcome is most likely related to your starting .gro file, the one with your initial configuration. The structure .gro files have a specific construction that must be respected, if I remember correctly the first line is free (usually the title of the system), second line must be the total number of atoms, then your listed system, and, as last line, the dimensions of the box. If you have a regular cubic box then the last line can just be 3 numbers, which are the length of the x, y, and z direction.
Hope this helps,
Nicola
- Badges
- Science topic
- Similar topics
- Filing