Hi,
> I am still wondering this issue. As you said, the internal potential of
> ligand is still remains. But as in State 0 (pro+lig), the energy is:
> V0=V_pro_internal+V_lig_internal+V_pro_lig, in state 1(pro), only
> V1=V_pro_internal remains. So the energy difference at lambda=1 equals
> V_pro_lig+V_lig. How do we include the ligand internal potential in ?
What you describe is a possible way to do this calculation, but a very
inefficient one. If you remove all ligand potentials, you turn your ligand
into an ideal gas and would have to correct that in the total energy by
reforming it from an ideal gas in vacuum in a separate step. This includes
a non-necessary ideal gas state that will never give you converged
energies. In usual practice, the ligand is not removed, but decoupled from
the system, so your V1 end state contains V_pro_internal + V_lig_internal,
equal to the solvated protein and the ligand in vacuum.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed Jan 04 2012 - 02:00:02 PST
