AMBER Archive (2000)

Subject: GB source code question

From: samantha hughes (s.j.hughes_at_ic.ac.uk)
Date: Wed Sep 20 2000 - 09:12:03 CDT

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
appreciated).

Thanks in anticipation,

Samantha

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Samantha Hughes
Department of Chemistry
Imperial College of Science, Technology and Medicine
Exhibition Road
South Kensington
SW7 2AY
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