[gmx-users] Hi

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 5 15:41:39 CEST 2006

santosh naik wrote:
> grompp -f em.mdp -c 5/out5.gro -p 1/out1.top -o 6/out6.tpr
> here the programme was failed showing the error
> Fatal error:
> No such moleculetype Na
> i have checked the ions .itp
> its having the information Na atom than why its showing this i could
> n't understand
> can any one help me over this here i have attatched my out6.gro file
> and the top file

gromacs is telling you the force field you are using doesn't have a 
molecule type of Na. This is distinct from an atom type of Na. Some 
force fields use SOD for the molecule type for sodium ions. Go and check 
the ions.itp file and adjust accordingly.

Adriana's reply might suggest why your minimization failed. Personally I 
wouldn't bother with PME for minimization, but I don't know whether 
switching to cut-off will help you.


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