Tricks in Gromacs

genion doesn't recognize SOL in top file

>Fatal error:

>No line with moleculetype 'SOL' found the [ molecules ] section of file 'topol.top'

Each type of molecule in your [ molecules ] section of your .top file must have a corresponding [ moleculetype ] section defined previously, either in the .top file or an included.itp file. See GROMACS Manual section 5.6.1 for the syntax description. Your .top file doesn't have such a definition for the indicated molecule. Check the contents of the relevant files, how you have named your molecules, and how you have tried to refer to them later. Pay attention to the status of #ifdef and / or #include statements.

From Gromacs error page

Or you probably have a non-Unix newline character somewhere. Run the .top file through dos2unix and try again.

From here.