[gmx-users] Ligand breaks during energy minimization

[Soumya Lipsa Rath]

Dear Justin and Nikhil,

Many thanks for your suggestions. Justin, I had optimized the parameters
using VMD's FFTK toolkit, so I just replaced my results in the *.str file
obtained from paramchem.

I tried minimizing the ligand in vaccum and in a solvent box, in both
cases, the molecule just scatters apart (pardon me, the bond doesn't
break).

I think there might be something wrong with the topology. However, I just
followed the general steps.

Thanks,
Soumya