[gmx-users] Incorrect number of parameters

[Mark Abraham]

On 3/05/2012 8:08 PM, Steven Neumann wrote:
> 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?

The simplest possible explanation is that your modifications to the .top 
are not as simple as you believe they are. Check that the original .top 
works as expected, and use the diff tool to compare the original and 
modified versions.

Mark