[gmx-users] OPLS specific problem in gromacs 4.5.4

[Ignacio Fernández Galván]

--- On Wed, 30/5/12, patrick wintrode <pat_wde2 at yahoo.com> wrote:

> After creating a box using editconf and then solvating using genbox, I try
> to add ions and get the infamous "number of coordinates in .gro does not
> match number of coordinates in topology" error.

I've had this problem after solvating a PDB that already contained waters. The genbox command reported that N waters should be added, but since there were already n waters in the PDB, it added only N-n waters to the topology, while it should have added the whole lot of N molecules. Changing the number in the .top file solved this.