Re: AMBER: question about delphi and UHBD

From: <>
Date: Tue, 28 Sep 2004 14:32:51 -0600

Dear Dr. Thomas Cheatham,

Thank you very much for your reply. I didn't mention the coulombic
energy difference(complex - receptor - ligand) in my previous email,
which is -302 kcal/mol in both programs. The final binding energy is
-37 kcal/mol in UHBD and 565 kcal/mol in delphi. The conversion from
kt/e to kcal/mol is correct and both are running with the same
internal/exterior dielectric. But it is a good suggestion to run a
really simple test case. I gonna try. Thanks again.



----- Original Message -----
From: "Thomas E. Cheatham, III" <>
Date: Tuesday, September 28, 2004 1:34 pm
Subject: Re: AMBER: question about delphi and UHBD

> Dr. Luo wrote:
> > Aside from different numerical implementations of molecular
> surface and
> > finite difference solvers, Delphi and UHBD also use very different
> > methods to compute reaction field energies. So in the end, you
> can't get
> > agreement at all for a complex molecule, such as a large protein.
> From the original e-mail of Shawn:
> > The final solvation energies for ligand, receptor and complex are
> > -1466, -1529 and -2730 kcal/mol in UHBD and -1035, -1056, -1224
> > kcal/mol in delphi.
> Despite the different algorithms used and the size of the systems
> beingstudied, I find it rather difficult to believe that these
> differences in
> energetics are reasonable between the two programs. One program
> suggestsa free energy difference of 265 kcal/mol and the other 867
> kcal/mol for
> the complex - (receptor + ligand) favoring the separated proteins.
> Both
> of these are completely unreasonable (if they are the final solvation
> energies). The disagreement between the two methods makes me
> wonder if
> the numbers are indeed comparable. Do the continuum solvation
> include anything else that you do not realize? Is the conversion
> reaction field energy to kcal/mol correct? Are both running with
> the same
> internal dielectric? Even generalized Born and continuum methods, in
> general, show better agreement than is seen between UHBD and
> delphi shown
> above leading me to speculate that something is amiss either in the
> running or interpretation of the results. I do not think this
> relates too
> heavily to the number of iterations.
> To test out your knowledge of delphi and UHBD, try running a
> really simple
> test case, like a continuum run on an isolated Na+; both programs
> shouldgive a number around 97 or so for the Na+ parameters (Aqvist
> adapted)present in AMBER.
> Good luck.
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Received on Tue Sep 28 2004 - 21:53:00 PDT
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