[gmx-users] genion -pname no NA molecule (sodium) type

Mark Abraham Mark.Abraham at anu.edu.au
Sat Mar 17 06:55:21 CET 2012

On 17/03/2012 4:48 PM, Wholly Peach wrote:
> Dear All,
> I use the following to neutralize the charge
> "genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8",
> Then I do the following "grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr"".
> However the feedback says there is no Na (sodium) moleculetype.

Your force field defines [moleculetype] sections for ions in its 
ions.itp file. Go and look at it, compare with your .top and see what 
the problem is. Atom names, residue names and moleculetype names are all 
different things, and each part of your .top must match the right name 
at the right time.

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