Question: Refinement And Energy Calculation Of Nucleic Acid Structures
2
gravatar for Angel
6.9 years ago by
Angel90
Angel90 wrote:

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?

modeling structural • 1.5k views
ADD COMMENTlink written 6.9 years ago by Angel90
0
gravatar for Pierre Poulain
6.9 years ago by
France
Pierre Poulain440 wrote:

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...)

ADD COMMENTlink written 6.9 years ago by Pierre Poulain440

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

ADD REPLYlink written 6.9 years ago by Angel90

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.

ADD REPLYlink written 6.9 years ago by Pierre Poulain440
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