GB source code question

From: samantha hughes <>
Date: Wed 20 Sep 2000 15:12:03 +0100

This is for any GB guru's out there:

In the source code GB.f in amber6/src/mm_pbsa/SOURCE there is a
factor called
epsfac used in calculating the Shielding energy contribution for
each atom.

In the code, epsfac is given as : epsfac=(1.-(epsint/eps))/2.
where epsint = 4 and eps is the epsilon value for the solvent of
interest (default eps= 80)

Thus epsfac = (1 -(4/eps)) /2

Now my problem is that in the papers by Jayaram et al
 (J Chem Phys, 109, 1998, 1465 and J.Phys.Chem.B, 102, 1998,
9571 )
the relevant factor is:

 (eps -4) /2

These two factors give very different results.

Does anyone know why the epsfac in the code is different to the
papers ? Alternatively, does anyone know who modified the
original code by Jayaram et al, to write GB.f so that I can
contact them directly ?? ( and an email address would be

Thanks in anticipation,


Samantha Hughes
Department of Chemistry
Imperial College of Science, Technology and Medicine
Exhibition Road
South Kensington
Received on Wed Sep 20 2000 - 07:12:03 PDT
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