[gmx-users] Speptide position restraint

[Christopher Tran]

Quoting Seonah Kim <kim at qtp.ufl.edu>:

> Dear All,
> 
> I'm having some problem about the position restraint.
> 
> I tried to run speptide example from Gromacs package.
> 
> When I typed
> Prompt>grompp -f pr.mdp -c speptide.gro -r speptide.gro -p speptide.top -o 
> speptide.tpr
> 
> I got the following errors at the end.
> 
> 
> 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
> turning all bonds into constraints...
> Excluding 2 bonded neighbours for SOL 850
> turning all bonds into constraints...
> processing coordinates...
> Fatal error: number of coordinates in coordinate file (speptide.gro, 191)
>              does not match topology (speptide.top, 2741)
> 
>
> Did I miss something to change before grompp?

Maybe the .gro file in your grompp command line hasn't been solvated?
Try genbox to add 850 water molecules to your .gro file.

 
> Thank you.
> 
> Seonah Kim.
> 
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