> 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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Received on Tue Sep 21 2010 - 11:00:03 PDT
