[gmx-users] ions different

[Mark Abraham]

> Dear experts,
> I have done upto minimization but faults in equilibration I am again
> starting the minimization, now in adding ions of sodium the following
> error is given, what is the reason for this.
> Warning: atom names in topol.top and ions.pdb don't match (NA - Na)
> Warning: atom names in topol.top and ions.pdb don't match (NA - Na)
> Warning: atom names in topol.top and ions.pdb don't match (NA - Na)
> Warning: atom names in topol.top and ions.pdb don't match (NA - Na)
> Warning: atom names in topol.top and ions.pdb don't match (NA - Na)
> WARNING 1 [file "topol.top", line 26779]:
>   5 non-matching atom names
>   atom names from topol.top will be used
>   atom names from ions.pdb will be ignored

This message seems clear and explicit to me. It is true that "NA" doesn't
match "Na" for a case-sensitive comparison. So like it tells you, the
"atom names" in your structure file don't match your topology. Computers
are literal, so you should get used to working reproducibly and
accurately. Curiously enough, that's good advice for science too! :-)

Mark