[gmx-users] Invalid order for directive bondtypes

[Atila Petrosian]

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?

How to solve this problem?