Planarity of the biphenyl ring is not maintained

Hi everyone,

I am working on a protein-ligand complex, and using Amberr99sb ff for protein and used acpype to generate ligand topology.
The ligand I have consist of 2 biphenyl rings (which should be planar) when I am running the simulation, I observed that the planarity of the biphenyl has been lost for reference I have attached the image of the molecule.
Can anyone suggest me what can be reason for the same?
I have also ran the ligand in water only environment but still the planarity is lost.

Thanks in advance

What command did you issued specifically? Have you use the correct charges and protonations? It could happen that ACPYPE/Antechamber may have not taken your rings as aromatic ones and so it wouldn’t apply the covalent bonds topology, hence no planarity.

I used:
acpype -i file.pdb -n 0

As the charge of the molecule is 0.
Along with all the hydrogens.
Is it correct?

How it can be corrected so that ACPYPE/Antechamber will take the rings as aromatic?