[gmx-users] genion error!

[Mark Abraham]

Qiang Zhong wrote:
> Dear users:
>      I want to prepare protein simulation on 0.15mol/l salt concentration,I use
> genion command to add ions,After genion,I change cln.top file last line to NA+
> 61,CL- 41.
>    When I execute grompp ,there are warning :
> 
> Warning: atom names in cln.top and cln_b4em.gro don't match (CL - Na)
> ........
> (more than 20 non-matching atom names)
> WARNING 1 [file "cln.top", line 9059]:
>   102 non-matching atom names
>   atom names from cln.top will be used
>   atom names from cln_b4em.gro will be ignored
> 
> I continue to execute "mdrun nice 0 -v -s cln_em.tpr -o minim_traj.trr -c
> minimized.gro -e minim_ener.edr",There are some error:

Hardly surprising... most gromacs warnings should be considered carefully.

First the atom names in your .gro and .top files have to match those in 
the .atp files for the force field you're using. Then check the order 
and number of Na and Cl are correct.

Mark