[gmx-users] OPLS specific problem in gromacs 4.5.4
Ignacio Fernández Galván
jellby at yahoo.com
Thu May 31 12:49:24 CEST 2012
--- 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.
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