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.
Mark
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