[gmx-users] Can you help me ?

[Mark Abraham]

job560 at sohu.com wrote:
> when I use the following command ,there always a error message.Can you 
> help me ? Thank you very much !
> 
> command: grompp -f em.mdp -c trp_b4em.gro -p trp.top -o trp_em.tpr
>                         
> 
> error message:
>    .
>    .
> creating statusfile for 1 node...
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
> checking input for internal consistency...
> calling /usr/bin/cpp...
> processing topology...
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein 1
> Excluding 3 bonded neighbours for IN4 1
> Excluding 2 bonded neighbours for SOL 4145
> Cleaning up temporary file gromppD2IkOr
> -------------------------------------------------------
> Program grompp, VERSION 3.3
> Source code file: toppush.c, line: 1264
> Fatal error:
> No such moleculetype Cl
> -------------------------------------------------------

Your topology is specifying a molecule type that doesn't appear in your
force field. Check that you've included "ions.itp" and that its contents
match your topology as far as atom and molecule names go.

Mark