[gmx-users] connectivity issue

[antonia vyrkou]

Hello,

I am a bit puzzled by the following problem

After the energy minimization,  in one type of molecules, appear two bonds
that should not exist. If I visualize the pdb before the minimization
everything is normal. After the minimization this problem appears.
I checked the ffbonded.itp, the aminoacids.rtp, and the the .itp files, and
all connectivity is normal.

Any ideas?