[gmx-users] Re: Atom names mismatch

[Low Soo Mei]

Hi,

Perhaps I am overlooking something very obvious in this, but was this 
really a log file (mdrun) error or a grompp error?

Manual entry for grompp says "grompp uses the atom names from the 
topology file. The atom names in the coordinate file (option -c) are 
only read to generate warnings when they do not match the atom names in 
the topology. Note that the atom names are irrelevant for the simulation 
as only the atom types are used for generating interaction parameters."

Cheers,
Soo Mei