[gmx-users] genion II

[Anton Feenstra]

Pedro Alexandre de Araujo Gomes Lapido Loureiro wrote:
> 
> "Warning: atom names in mshion.top and mshion1-1.gro don't match (Cl - OW)
> ...
> (more than 20 non-matching atom names)
> Warning 7 [file "mshion.top", line 33]:
>   33145 non-matching atom names
>   atom names from mshion.top will be used
>   atom names from mshion1-1.gro will be ingnored"
> 
> In the .top file I had already added one Cl atom and deleted one water
> molecule.
> Am I doing somethig wrong?

Apparently you don't have the same order of molecules (and thus atoms) 
in your .gro file. This causes the atom name mismatches. You should feel
lucky, since previous versions of Gromacs did not even check this!
I don't know whether genion adds your ion before or after the water 
molecules, but assuming it puts it before, then your .top file should 
end in something like this:

[ molecules ] 
Protein		1
Cl		1
SOL		4687


The order is absolutely important!


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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