AMBER Archive (2003)

Subject: solvent free energy, GB

From: Robert G. Endres (endresrg_at_ornl.gov)
Date: Thu Jan 16 2003 - 15:33:36 CST

Hi AMBER users,

when using the generalized Born (GB) implicit water model (igb>0 in
sanders), it is not exactly clear to me what the options "gbsa"
(calculates surface area which is then included in the solvation term) and
"surften" (nonpolar contribution to free energy from solvation using
these surfaces) do additionally to the GB model itself.

Correct me if I am wrong: the GB is used to calculate the contributions to
the free energy of solvation for charged atoms, the "surften" is the
contribution from uncharged atoms? So one should always use both together
if the time for calculating the surface is not an issue? (Does anyone know
estimates of relative magnitudes for both?)

Thanks for any insights in advance.

Best regards,
  -Robert