GROMACS version: 2020.4
Dear users,
I’m modelling a system containing a protein near an ice layer (tip4p water model, charmm27 ff) and have some issues. When I wanted to add ions to the system, I had an error telling me that number of coordinates in my coordinate file does not match topology (there are more atoms in .gro file). So, I’ve found that pdb2gmx adds ‘M’ atom to each ice water molecule. There is already dummy atom along with oxygen and two hydrogens in my .pdb input file (all names are consistent with the force field naming). So why does pdb2gmx add an additional ‘M’ particle if there is one already?
I deleted the lines with ‘M’ atoms and everything works fine. But I still want to know why this happens. Probably somebody encountered same situation.
Thank you!