Can I simulate 2 proteins and 1 ligand?

User discussions
1

GROMACS version:
GROMACS modification: Yes/No

I am testing MD simulation of Tri-complex structure published in PDB. Only A and D chains are used, PDB: 9AX6

I have previously tested other samples through Protein-ligand tutorial and thought it would be feasible.
( tutorial : Protein-Ligand Complex )

However, I get the following error in NVT equilibrium.

Internal error (bug):
Step 0: The total potential energy is 5.84329e+25, which is extremely high.
The LJ and electrostatic contributions to the energy are 5.84329e+25 and
-906647, respectively. A very high potential energy can be caused by
overlapping interactions in bonded interactions or very large coordinate
values. Usually this is caused by a badly- or non-equilibrated initial
configuration, incorrect interactions or parameters in the topology.

Is there anything I need to fix in energy minimization or equilibrium?

2

I solved it before I got the answer.

All the process worked fine even though it matched the tutorial, the reason for the error was that I had to write the ligand topology before the water topology.

Hope it helps.

3

I am also working on a tri complex system and i am facing the same error in my equilibration.