Dear Gmx Users, I run the simulation of protein-ligand complex. Then I extracted coordinates for SMD - I want to pull away my ligand. I used to topology from pevious simulation, so I removed water, ions from topol.top as the size box will be changed etc. I placed protein-ligan in new box and solvated the system. Now I want to proceed to add ions:
grompp -f minim.mdp -c Solv1.gro -p topol1.top -o ions1.tpr Fatal error: Incorrect number of parameters - found 3, expected 2 or 4 for LJ-14. Well there is nothing wrong with the topology files as I took them from previus simulation just removing water and ions. I think that Gromacs does not read whole file... Have you ever had such problem? I will appreciate any help, Steven
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