The weak CH-pi hydrogen bond has currently been highlighted in biomolecules. I am interested in monitoring/calculating CH-pi interactions (if present between sidechains of aromatic residue and aliphatic hydrophobic residues) in my simulation. Is there a tool to calculate the presence of these interactions either from a pdb file or a trajectory and hence calculate their occupancy?
Check this paper DOI:10.1007/s00894-014-2136-5
In cpptraj you can do it with distance and angle cmd
Dear Neha,
in principle you can't, due to the absence of electronic effects. You can indicate the possibility of this interaction by measuring distances and comparing these distances to those derived from quantum mechanical calculations, or you can retrieve frames from your simulation and submit it to semi-empirical (using modern hamiltonians as RM1 for the entire protein) or ab initio/dft (for parts of the protein) calculations and then look, for example, to bond orders between the interacting atoms. In the other hand, you can run the MD using a hybrid QM/MM approach, in which you set part of your system to be handled by quantum mechanical strategy.
It is important to point that, while molecular mechanics are not supposed to describe pi-interactions (such as pi-hydrogen bonds, pi-stacking, pi-OH interaction, cation pi and so on), some works indicated that the interaction energy derived from molecular mechanics is in fact very well correlated to those from quantum calculations. While unexpected, this may be due to the empirical adjustment of force fields, and could potentially result in a limited difference in the molecular system simulated using the QM/MM approach.
Good luck with your calculations!
Regards,
Hugo
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