[gmx-users] Ligand breaks during energy minimization

Soumya Lipsa Rath soumyalipsabt at gmail.com
Sat Mar 26 01:03:50 CET 2016

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

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


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