I was running the command gmx grompp -f ions.mdp -c 1ua7_solv.gro -p topol.top -o ions.tpr -maxwarn 1 but I encountered an error stating number of coordinates in coordinate file (1ua7_solv.gro, 90855) does not match topology (topol.top, 90854). How to overcome this . Please help me out . I am attaching both the files and screenshot of the error.
The answer to this error is always “you haven’t been keeping track of what is in your system correctly.” If all you’ve got is a protein (or some solute) in water, let gmx solvate update the topology with -p. If you have other entities in your system that require manual updating in the topology, you simply need to take great care to do this properly.
Don’t do this :) Trust me, in 99.9% of cases, you’ll regret it.