[gmx-users] Invalid order for directive bondtypes

Mark Abraham mark.j.abraham at gmail.com
Mon Oct 6 16:20:41 CEST 2014

On Oct 6, 2014 3:57 PM, "Atila Petrosian" <atila.petrosian at gmail.com> wrote:
> Dear Mark
> Very thanks for you reply.
> I solved previous problem by swapping the order of my #include statements
> in forcefield.itp file.
> I used grompp for energy minimization, I obtained em.tpr file without any
> problem. Then I used mdrun for energy minimization, this step was done
> without error, but, when I see gro file obtained from minimization using
> VMD, there is unusual state. Those figures related to this state are in
> following links:
> https://www.dropbox.com/s/ofyknhton3cmelp/figure.TIF?dl=0
> https://www.dropbox.com/s/g71xgjolka9x0v4/figureII.TIF?dl=0
> What is the reason of this state?

No connectivity is present in a .gro file. How is VMD supposed to present
information that isn't there? It guesses, assuming the file contains a
protein, as discussed in every second post here that concerns VMD. Your
.top file is definitive. Google will show a few tools that might help here.

> How to solve this problem?

Understand what your tools do! :-)


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