[gmx-users] Error in .top file for grompp

[Mark Abraham]

한상화 wrote:
> Dear Gromacs users,
> 
>  
> 
> I have gone through all the way to the final product MD, where I 
> received the following error message for grompp.
> 
> The same topology file pn.top did not give me any problem in the 
> previous steps including grompp with pr.mdp or grompp with em.mdp.

The problem doesn't look like it's actually the topology... that was
just the last thing that grompp looked at.

> I included solvent and ions in the md.mdp file for temperature control.
> 
> Any comments would be greatly appreciated.

> *[root at cc papain]# grompp -f md.mdp -c pn_md.pdb -r pn_md.pdb -p pn.top 
> -o pn_md.tpr*

This isn't your problem, but it is a *really bad idea* to do daily work
as root. See here for info and discussion why...
http://en.wikipedia.org/wiki/Superuser

> 
> ' for variable integrator, using 'md'
> 
> Next time use one of: 'md' 'steep' 'cg' 'bd' 'sd' 'nm' 'l-bfgs' 'tpi'
> 
> ' for variable ns-type, using 'Grid'
> 
> Next time use one of: 'Grid' 'Simple'
> 
> ' for variable coulombtype, using 'Cut-off'
> 
> Next time use one of: 'Cut-off' 'Reaction-Field' 
> 'Generalized-Reaction-Field' 'PME' 'Ewald' 'PPPM' 'Poisson' 'Switch' 
> 'Shift' 'User' 'Generalized-Born' 'Reaction-Field-nec' 'Encad-shift' 
> 'PME-User'
> 
> ' for variable optimize_fft, using 'no'
> 
> Next time use one of: 'no' 'yes'
> 
> ' for variable tcoupl, using 'No'
> 
> Next time use one of: 'No' 'Berendsen' 'Nose-Hoover' 'yes' 'Andersen' 
> 'Andersen-interval'
> 
> ' for variable Pcoupl, using 'No'
> 
> Next time use one of: 'No' 'Berendsen' 'Parrinello-Rahman' 'Isotropic'
> 
> ' for variable gen-vel, using 'no'
> 
> Next time use one of: 'no' 'yes'
> 
> ' for variable constraints, using 'none'
> 
> Next time use one of: 'none' 'h-bonds' 'all-bonds' 'h-angles' 'all-angles'
> 
>  
> 
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#
> 
> WARNING 1 [file pn_md.mdp, line unknown]:
> 
>   Unknown left-hand 'warnings' in parameter file
> 

This is being caused by gibberish in your .mdp file. Fix that first.

Mark