[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.
Mark
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