[gmx-users] topology doesnt match

[Mark Abraham]

Robert Selwyne wrote:
> Dear GMX users
> When i tried to rum grompp i get these errors. Would any one be able to
> sort out this problem?
> Sincerely
> Robert
> -------------------------------------------------------------------------------------------------
> grompp -v -f adp.mdp -po adpmdout.mdp -c genbox.gro -p genbox.top -o
> gromppout.tpr

It would be easier to answer your question if you'd told us what you did 
to generate genbox.gro and genbox.top. As it is, I'm going to have to guess.

> creating statusfile for 1 node...
> 
> Back Off! I just backed up adpmdout.mdp to ./#adpmdout.mdp.1#
> checking input for internal consistency...
> calling /lib/cpp...
> processing topology...
> Generated 279 of the 1225 non-bonded parameter combinations
> Excluding 3 bonded neighbours for Protein 1
> WARNING 1 [file "genbox.top", line 283]:
>   System has non-zero total charge: -3.000000e+00
> 
> processing coordinates...
> Fatal error: number of coordinates in coordinate file (genbox.gro, 3516)
>              does not match topology (genbox.top, 33)

I guess that you've added solvent, and not updated the [molecules] 
section of the .top file. Check chapter 5 of the manual if you don't 
know how to do this or what I mean :-)

Mark