I am using gromacs 4.5.3 version.
I am doing simulation of Protein-Ligand complex. My all system is right but I have confusion related to Planarity aromatic ring.
My ligand have 3 aromatics ring.
I have generated .itp file from Prodrg and i have setup very well.
My ligand planer/flat(3 phenyl ring) during EM/NVT/NPT but after given mdrun I have given for 10 ns.
I have dump pdb file at 1ns but my ligand lost planer structure.
I have lot of question related to Ligand and Protein ?
1. Have any problem with protein-ligand H-bond interaction ?
2. As per chemistry aromatics structure should have remain planer ?
3. Any problem with simulation ?
4. sily question- If aromatics structure bent then any problem with Protein-ligand interaction/ Binding site ?
Hope I will get best answer.
Thanks In advance