Refinement And Energy Calculation Of Nucleic Acid Structures

Question

[Angel]

Hi Biostars!

Very few papers are available regarding energy minimization and energy calculation of nucleic acid models using Charmm27 force field. So, i couldn't clarify my doubts doing literature search. Could anyone please clarify

How energy minimization and energy calculation of nucleic acid models is different from energy minimization of protein models and is it necessary to setup a explicit solvent for energy minimization of nucleic acid structures?

Answer 1

[Pierre Poulain]

In principle, energy minimization should not be different for nucleic acids and proteins since it is based on several evaluations of the first or second derivatives of the energy, whatever the energy actually is.

The energy calculation however depends on the forcefield being used and the latter captures the physics of the system. So yes, forcefields could be different for nucleic acids and proteins (at least parameters for van der Waals, électrostatics, angles...)

[Angel]

Thanks @Pierre. what about necessity to setup a explicit solvent for minimization?

[Pierre Poulain]

Maybe because the phosphate backbone of nucleic acids is highly charged and interactions with water molecules are important. However, keep in mind that atom movements generated by energy minimization are rarely of large amplitude.