[gmx-users] Regarding phenyl rings absolutely flat.

[HARESH AJANI]

Hello Dear, 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

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