Hi,
as Bill already wrote, the total potential energy of the protein is not
what you want if you are comparing the stability of two solvated
conformers. The total free energy change upon changing the conformation is
much more useful here. This sounds like a perfect application for MM-PBSA,
check out the examples in the MMPBSA directory of amber, one of them does
exactly what you probably want.
Kind Regards,
Thomas
On Tue, September 21, 2010 1:42 pm, Bill Ross wrote:
>> I have completed two solvent explicit simulations for two possible
>> conformations of my protein. In order to know which one is more stable,
>> I need to compute the total potential energy form my protein
>> without solvent.
>
> This might tell you which was more stable in vacuum. Is that useful?
> E.g. the conformations may not even be attainable in vacuum.
>
> Bearing in mind that you may be on the wrong track, it is possible
> to get the energy of the solute alone by extracting the coordinates
> for just those atoms with ptraj, e.g. into pdb, then loadpdb and
> saveamberparm to create a prmtop/inpcrd, and run a single-step
> energy minimization.
>
> Bill
>
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>
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue Sep 21 2010 - 21:30:03 PDT
