[gmx-users] gro does not match top

[Shima Arasteh]

Hi,

I am solving a protein in water. This protein has a charge of +3.
After solvation there is 3272 water molecules.

Next, I use genion command to add NACL 1M and 3 extra CL ions to neutralize the system.
#genion -s ions.tpr -o cyclic_solv_ions.gro -p topol.top -nname CL -nn 3 -conc 1

After this, the top file shows:
 Protein_chain_A     1

SOL         3147
NA               61
CL               61
CL               3

But when I check the cyclic_solv_ions.gro file, there are 60 NA and 60 CL ions! Therefore the top doesnt match with gro file and I get the fatal error.
What' s your suggestions? How does it come? 

Thanks in advance.



Sincerely,
Shima