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
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