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From: Hector Chang <chang52.purdue.edu>

Date: Fri, 20 Aug 2010 16:17:44 -0400

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

Date: Fri, 20 Aug 2010 16:17:44 -0400

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Fri Aug 20 2010 - 13:30:03 PDT

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