Planarity of the biphenyl ring is not maintained

User discussions
1

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

non-planar
non-planar1280×651 73.7 KB

2

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.

3

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?