Hi,
I want to calculate the value for the two terms added into the vacuum potential
function. My question is the description of the variables and where I can find
these values. I'm running a 3 atoms system (CA, C, O - no bonds) to check my
calculation with AMBER. Correct me if I'm wrong, the "epsilon" is the dielectric
constant of the solvent (ex. water = 78.8), q is the charge (obtained from the
"parm99.dat") and "rij" is the separation between two atoms. My problem is the
"Ri & Rj" - effective Born Radii for "fGB function" (where I get these values?),
for the surface area model, "A" & "sigma" (how can I get these values?).
I was looking in the AMBER manual and in the literature about effective Born
Radii values, but most of the information talks about how to calculate it. I did
the "rbornstat" input in AMBER. The purpose is that I want to know how AMBER
calculates the last two terms when it is in implicit solvent. I want to
calculate it myself by hand.
Thanks a Lot,
Hector
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Received on Fri Aug 20 2010 - 13:30:03 PDT
