[gmx-users] AMBER99sb-ILDN force field and TIP4P water model

[Mahboobeh Eslami]

Hi GMX Users, please help me
I am trying to begin a simulation of a protein and ligand coplex by gromacs4.6.3.

I am using AMBER99sb-ILDN force field and TIP4P water model. However,
I am facing a problem in the ion adding step.

when  I issue the grompp command to generate the necessary .tpr file
for simulation to be utilised by genion tool, I get the following
error :

Fatal error:
number of coordinates in coordinate file (solv.gro, 102546)
does not match topology (topol.top, 133916)

whe i use tip3p, i don't get error.

Thank you very much