[AMBER] Quantifying Errors in PBSA

From: D.J. Cole <djc56.cam.ac.uk>
Date: 05 Mar 2010 19:47:45 +0000

Dear Amber users,

I am interested in calculating the error introduced in calculating the
absolute binding energy (DG) between two small peptides (~30 atoms) when
using the AMBER force field and the PB implicit solvent model compared with
an accurate quantum chemistry calculation. I know that most quantum
chemistry codes use the PCM implicit solvent model (I'm using Gaussian03)
and that absolute DGs are very dependent on the parameters of the PCM
model. However, I'm not interested in the errors in the solvation model,
just in the errors introduced by treating the system as a set of partial
charges in AMBER rather than using the optimised wave function etc.

So I basically want to make my PCM calculation as close to the PB
calculation as possible. I get a good preliminary match using Bondi radii
in PCM rather than the default UA0 (are Bondi radii the default in PB
calculations in AMBER10?). Is there anything else I can do to improve the
match between the two models, such as the way the solute/solvent interface
is defined, or is this a hopeless exercise?

If this has been done before I'd be very grateful for some references.

Many thanks,

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Received on Fri Mar 05 2010 - 12:00:03 PST
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